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In Mojave, as observed, pressing the red cross will close the window but the indicator dot remains present until Messages.app is no longer the foreground app - i.e. clicking anywhere on the screen will result in the app closing.
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I can finally remove Messages from my (start hidden) login items to avoid me missing new messages.

EDIT: For what it's worth, I notice Calendar.app has a similar behaviour once the window is closed - the indicator dot disappears once its no longer in the foreground.

For me, closing all messages windows and then clicking around elsewhere definitely does not result in the messages app closing. I can still see it running in Activity Monitor and when doing ps in Terminal. The PID remains the same, meaning it has not been quit or relaunched at any point. So, I'm not sure what's going on because I do believe other people are seeing different behaviour to this. Calendar also does not quit for me and instead stays open all the time same as Messages and all other apps.

By the way, Messages.app has supported remote push notifications for a long time now. This is definitely not new in Mojave, and has been around since at least Sierra and I think long before that even. So you haven't had to have it autolaunch for quite a while.
 
For me, closing all messages windows and then clicking around elsewhere definitely does not result in the messages app closing. I can still see it running in Activity Monitor and when doing ps in Terminal. The PID remains the same, meaning it has not been quit or relaunched at any point. So, I'm not sure what's going on because I do believe other people are seeing different behaviour to this. Calendar also does not quit for me and instead stays open all the time same as Messages and all other apps.

By the way, Messages.app has supported remote push notifications for a long time now. This is definitely not new in Mojave, and has been around since at least Sierra and I think long before that even. So you haven't had to have it autolaunch for quite a while.

Apologies I should have been clearer and said that Messages.app appears to not be running (e.g. app indicator dot goes away) - having checked Activity Monitor I can see it remains running when closing the window and clicking away - it looks like its quit but as you said, its still running. However, if you CMD+Q Message.app, it disappears from Activity Monitor. In this scenario, message notifications and (more importantly) the unread counter on app icon continue to show. Upon launching Messages.app it has a new PID.

The behaviour has definitely changed - In my previous Sierra and HS installations across multiple machines Messages.app needed to be running for the unread counter on app icon to show - like the Mail.app behaviour.

What I'm getting at is I think that they have changed how the app functions behind the scenes. I am certain that previously the unread count app icon would disappear when Messages.app was quit, now it remains - like the Reminders.app behaviour.
 
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Messages.app appears to not be running (e.g. app indicator dot goes away)

I don't know why it's different on mine but I've tried multiple times now over many days and my Messages dot never disappears from the dock unless I actually quit Messages. No matter if I close all the Messages windows and get on with my day doing other stuff it still sits in the Dock with the running indicator dot underneath.
 
EDIT: For what it's worth, I notice Calendar.app has a similar behaviour once the window is closed - the indicator dot disappears once its no longer in the foreground.[/QUOTE]

With my experience on previous versions of macOS, I would still receive Messages even if app was not open (quit etc).

Just don't like how when you close the Messages window now and switch to another app, Messages actually quits as opposed to just hiding the window so now when I wish to read a new message, the app has to go through the open sequence (few seconds) before opening. Feels like a bug to me.

Mail seems off too. Reply and forward icons next to email messages on your messages list do not appear until you change to a different section, then back again.
 
Looking at it some more, I don't think it's actually closing. I think the dot underneath is disappearing, but I think the app is still open in the background as before. I'm still getting notifications when I get a message, even though it appears that the app is closed. In previous releases, if the app was completely closed with no dot underneath, I wouldn't get any notifications for incoming messages, so I think it's a bug in Mojave that the dot is disappearing.

Alright, it looks like it doesn't actually close but the dot disappears from underneath the dock icon. As soon as I click the Messages icon the window pops up immediately without a single bounce. However, if I actually go ahead and quit the application properly it bounces once before the messages window appears.

Looks like a bug to me.

Exactly. And Messages is not terminating. Instead, the indicator simply disappears but the application continues to run in the background nevertheless. Thus, it behaves completely irrational and unlike every other application I've encountered.

It doesn't terminate, but the indicator in the dock disappears once I switch to another workspace.

I don't think this is entirely true either, at least not for me. This behavior is driving me crazy. If I close the window and it loses focus, the dot goes away. If I click the icon within a short period of time, the window comes back along with the dot. If I come back after a longer period of time, clicking the icon causes it to bounce and reopen the application, as noted, taking several seconds longer. And if I haven't left the window open when the computer sleeps, the app is closed when I wake it up.
 
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This is definitely a bug because the Messages icon disappears from the Command+Tab app switcher. Not to mention the icon bounce I get when it's re-opening. Very annoying!
 
iMovie, TextEdit, Keynote, Pages, Calendar, Books, FaceTime, Notes, Maps all do that on my machine. Not sure if some of them used to behave differently — I don't use those that much.
 
Definitely a bug.. CMD W or Q now have the same function. I like to close windows but leave apps open! 1Password for example, now it bounces when I click it (i.e. it closed the app)
 
Just don't like how when you close the Messages window now and switch to another app, Messages actually quits as opposed to just hiding the window so now when I wish to read a new message, the app has to go through the open sequence (few seconds) before opening. Feels like a bug to me.

Same experience here. Whether it is technically quitting/terminating or not, I don't care. The experience of having to wait for it to reopen it the concern as I use messages all day (and would much prefer not to keep it visible as I often screen share, hence why I click the red button).
 
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I also notice this behavior happening on my end as well. On both my Macbook and iMac. It isn't always like this, I would say it happens about 75% of the time though. Not sure why it's behaving inconsistently like this.
 
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I don't know why it's different on mine but I've tried multiple times now over many days and my Messages dot never disappears from the dock unless I actually quit Messages. No matter if I close all the Messages windows and get on with my day doing other stuff it still sits in the Dock with the running indicator dot underneath.

Same here. Nothing I try to do (clicking on the desktop, switching to other apps (windowed and full screen), even waiting 5 minutes) makes the dot disappear under Messages after I close its window. This is on a 2014 Mac Mini with 8GB of RAM. I'll try on my other Macs later to see if the behavior is different on them.

Edit: Going to add to this post as I check my different Macs:

2014 Mac Mini - i5 8GB: Dot stays after closing messages window, never disappears
2009 Mac Pro (flashed to 2010) - 6-core Xeon 24GB: Dot disappears after closing messages window and clicking on the desktop
2015 MacBook Pro 15" - i7 16GB: Dot disappears

Wow, no pattern to this so far!
 
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As someone here has mentioned about other apps, what I have noticed that apps that used to quit after the last window was closed now no longer do. On my iMac: Preview Pages, Numbers and Text Edit are all still running (with the Dock Dot), but none have any windows open. This is a change from previous OSes.

These are all Apple apps. Non-Apple apps such as Movist quit immediately the window is closed.
 
As someone here has mentioned about other apps, what I have noticed that apps that used to quit after the last window was closed now no longer do. On my iMac: Preview Pages, Numbers and Text Edit are all still running (with the Dock Dot), but none have any windows open. This is a change from previous OSes.

These are all Apple apps. Non-Apple apps such as Movist quit immediately the window is closed.

I use MS Office so I don't use Numbers and rarely Text Edit, so I can't speak to those, but Preview always required me to quit the app, even back to Yosemite where I first started using Macs.
 
Created an account just to say "me too". Kidding aside, I'm seeing the same behavior hence the reason I'm here from our magical Google guru. CMD + H for hiding the app seems to be my workaround for now.

Steps to reproduce:
- Open iMessages
- Communicate
- Close window using little red X
- Black dot on Dock stays until switching to another app
- Switching back to iMessages within a certain amount of time does not need to "re-open" app.
- Waiting longer than certain amount of time requires the app to re-open, and we lose precious time waiting.
- Compare results.

Machine: iMac (Retina 5K, 27-inch, 2017)
OS: 10.14 (18A391)
 
Not questioning the buggy nature of this, but genuinely curious -- for those of you who are closing an app's sole window and wanting it to keep running: why not just hide the app instead (⌘+H), or minimize it to the dock?
 
Just tried this and it worked for me. My Air was doing it, but my iMac wasn't. No way I could have kept on going with it quitting every time I close it. Hopefully this works for others.

Disable Automatic Termination in Mac OS X

Launch Terminal and enter the following defaults write command:

defaults write -g NSDisableAutomaticTermination -bool yes

Remember to restart iMessage afterward.

-RC


Source:
http://osxdaily.com/2012/05/15/disable-automatic-termination-of-apps-in-mac-os-x/
 
Just tried this and it worked for me. My Air was doing it, but my iMac wasn't. No way I could have kept on going with it quitting every time I close it. Hopefully this works for others.

Disable Automatic Termination in Mac OS X

Launch Terminal and enter the following defaults write command:

defaults write -g NSDisableAutomaticTermination -bool yes

Well that's it! That default was probably set in Lion or Mountain Lion but removed sometime afterwards. So if you fresh installed Mojave then you probably won't have been getting the quitting, but if you have been upgrading since 2012/2013 then you would have been seeing this quitting.
 
Well that's it! That default was probably set in Lion or Mountain Lion but removed sometime afterwards. So if you fresh installed Mojave then you probably won't have been getting the quitting, but if you have been upgrading since 2012/2013 then you would have been seeing this quitting.

So is there a negative impact to disabling automatic termination? Anything to caution me about before doing this?

This iMessage issue has been driving me crazy. I habitually hate CMD+W to close the window, and always use CMD+Tab to toggle back to the application. Whether it's still "running" or not is moot... if its not in the toggle bar when using CMD+Tab, it's a pain.
 
So is there a negative impact to disabling automatic termination? Anything to caution me about before doing this?

Since the default on a fresh install is for it not to quit then there should be no negative affects, you are just returning to the default setting. It's only a hidden plist setting anyway so you can always change it back very easily if needed.
 
After a while the indicator disappears, but when clicking the Messages Dock icon it doesn't bounce and the main window appears instantly. After quitting the app it does bounce once.
 
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