I think that's when you have an update in App Store, I tried one of the apps, and after it updates, the red dot is gone. For the "Settings" app, I think you might have some incomplete process I guess, but also some of my apps have updates but don't show red dots, I know if an app already in dock, it won't show red dots, but I do have some apps that have updates that are not in the dock doesn't show red dots, for example, WWDC app (currently called "Apple Developer") has updates in App Store, and I didn't put in the dock after I launch this app, go back to the home screen it does not have the red dot, I think it's happening rarely. (here is the truth, I just updated all the apps, some red dot are gone, some aren't gone, I am not sure why)