With Gnome Shell 46.4, the indicators for running apps shown in the Overview/Dash (not Dash to Dock) are appearing over the icons rather than below. See image.
I was able to fix the overlapping by changing the counters indicator in Dash to Dock settings. Im currently using “Dashes”
Dash-to-Dock is disabled. This is the Gnome Dash, which has no settings.
This might be best directed to Gnome, unless it’s a theming issue. Are you using the default theme without modification?
I’m not a Gnome user, so cannot help with troubleshooting. Given time, someone else might have an idea or two.
Cheers.
This is basically the solution, as I can’t reproduce it with the default Adwaita theme and icons.
From your picture it is obvious that a different theme (or at least a different icon set) is in use, so please try to reproduce it with Adwaita.
In case this is the Manjaro default, please report it on their Gitlab.
I set the icon theme back to Adwaita (default). The problem is the same.
Note:
If you are using Dash-to-Dock extension, then you need to temporarily disable Dash-to-Dock to have the Dash appear in the Activities Overview. It is always at the bottom. Do you see this problem?
I would suggest to disable all extensions, set the default theme(s) and reboot, or at least log out/in.
If that really doesn’t help, create a new user account and check if the issue persists.
I don’t use D-t-D, so I can’t comment on that.
Extensions like D-t-D which change a lot of the desktop, can do a lot harm to your system, as they leave traces in the gsettings even if you disable them. The last resort would be to reset gsettings.
I don’t use Dash to Dock either. The reason I mentioned disabling it is because if you use it, the Dash doesn’t appear at all on the Activities Overview; Dash to dock is in it’s place and you would not see this problem.
The Dash is an integral part of gnome-shell, and Dash to Dock is a gnome-shell extension.
If I use Dash to Dock, this problem is not apparent. I did check that.
Of my 3 Manjaro installations, I see that the 2 older ones are both affected. These are both probably 5 years old. The newer one, installed maybe a year ago, does not have this problem. All up to date.
I will leave it at that. Thanks for the suggestions and trying to help out.
Update: I decided to just use Dash to Dock. It will be fine.