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I had this happen when I first updated to ios9 on my 5s. Since updating to 9.1 beta on both that phone and my new 6s it hasn't happened again.
 
It's a known iOS 9 bug. The best solution for fixing it is to go into Message settings and turn character count on/off. It then goes away and doesn't come back.

I tested him with this info and he says that Character count is OFF.

It looks to me like a voice message box but it should not stay in the way of your text string like this.
 
Wife's 5S having the same problem but only on NON-iMessage messages. I was temporarily using an old Android phone after selling my 6 and while waiting for my 6S and it kept happening to her on my texts. Now that I am back on the 6S it has completely stopped.
 
It seems that this is a bug with the "Raise to listen" feature.

I have to admit, I was stumped when I read this thread yesterday until it happened to me today.

What happened was I set the phone down in my car seat and my leg covered the proximity sensor. When I moved my leg, I notice my screen lit up and there was that 0:00 second voice message like pictured.

I tried to recreate the issue, but I couldn't get it to do it. I'm still pretty sure Raise to Listen is somehow responsible, though.

You can disable it in settings>messages. Let me know if that fixed the problem!
 
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Update. I have had my VP try all the above and nothing stops it from coming back. I have been to Apple's site and filled out the error report. The 9.0.2 update did not fix it.

His 6S does it yet my 6S+ had not had a single problem.
 
go to task switcher, close messages and reopen. no need to restart phone. Happens to me every now and then.
 
Happened to me once. I think I accidentally tapped the text to speech or recording to send text? While I rotated from landscape to portrait and it was glitched like that.
To fix it, restart the app (close the app via multitasking menu and open it again).
 
It's happening to me too...it's annoying. Just have to close and reopen the app to get rid of it.
 
It's happening to me too...it's annoying. Just have to close and reopen the app to get rid of it.

My VP's 6S is still doing the same thing. Sometimes closing and reopening the app does not remove the grey box from the text field. Doing the latest updates and nothing has stopped it. Rebooting the phone can make it stop for an hour or day, you never know.
 
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