macOS Sierra Dock open app indicator missing
I've seen that happen when a system isn't logged out for months, so the first thing I would do is save work and then log out.

When you log back in, consider holding the shift key (or not having all the apps re-start) as well if a quick log out and log in don't clean things.


On rare occasion the saved application state gets messed up and a cleaner log in can help.
On other rare occasions it’s genie effect and software bugs - Visual bug in Dock after macOS Mojave installation
Be sure it’s not just a display failure as well. I would rule that in or out with some tests below:


Start with logging out and then restarting with no accounts logged in. Should you have something you can reproduce right after a restart, would be when I would get a sysdiagnose of the dock process and get a support ticket in to Apple.

Lastly, since you were removing preference files from under the preference database engine, consider trying a new user account to be sure things are good. In that case, you can consider moving files and settings over to a new account or know that it's just a user library preference corruption issue.

If you reproduce this on a new account, a backup and reinstall of the OS would be my next step. Hopefully you don't need to do an erase install, so start with an in-place reinstall where your user data isn't erased.