some icons don't have menus and are drawn differently
I'm using this extension on two computers and for some reason the problem only occurs on one, even with the same versions (Gnome 43.3, extension v47). The main difference is that on one I run Ubuntu as a distribution and on another Fedora. Both use the Gnome session. The issue is on my Fedora installation. A couple of weeks ago, some icons stopped having a menu and opened the application on click. (Signal Messenger installed from Flathub). Also, the icon produces an artifact when it's moved (see screenshots)

At the same time, another icon appeared (Protonmail Bridge installed form Flathub) appeared. I believe it wasn't shown before because it doesn't have a menu at all. This doesn't bother me much, but the double drawn icons are quite annoying.
I tried disabling all other extensions, but the behavior remained the same.
So looks like you're getting both the indicator and the tray icon indicators... I'm keen to add an option to disable legacy tray icons, a part from some known old apps maybe
Thanks for the answer. Do you know what might have been the reason for the change in behavior? The Signal indicator worked perfectly until last week or so.
It could depend on the libappindicator or libayatana indicator behavior more than on us, as we expose both support for legacy tray icons and AppIndicator icons.
New version exposes a setting to disable legacy tray icons, see if that helps your case.
Thanks, it helps a bit, but it disables the icon (Signal) entirely. Before, the Signal icon wasn't a legacy icon, but it's the same application. Is there some process that converts legacy icons to AppIndicator icons? If yes, it seems it doesn't work in my case.
After a reboot, the Signal icon is handled by the AppIndicator library. It seems the Signal icon works as legacy icon as well as AppIndicator and maybe libayatana “grabbed” the Indicator first.