On GNOME there are usually programs without icons for the windows. Most such problems are related to the StartupWMClass. But sometimes it’s unclear how to fix it.
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I use GNOME’s looking glass (ALT+F2 → lg → Windows) to inspect wmclasses.
Missing icons are usually either due to a doubly wrapped executable (ie. the wmclass erroneously contains a dot prefix) or it simply doesn’t match the .desktop entry at all.
Searching for StartupWMClass on the bug tracker provides examples of how to fix it.
I just encountered a weird case. When I change the StartupWMClass of SafeEyes, the wm class in lg is also changed. Not sure if it’s a wayland problem. And JabRef has icon, but the wm class doesn’t match the StartupWMClass.