To add to this, I’ve also experienced this; I assume it’s somehow related to BAMF (or whatever it is tha tracks windows these days) failing to identify the icon (from a desktop file which now points at /snap/snapname/1.5/executable) with running instances of the app (/snap/snapname/1.4/executable or whatever). It’s both confusing and annoying; there’s no way to see a list of running instances of the application by clicking on the Dock icon.
The dock in question is that in the stock Ubuntu GNOME desktop (Dash-to-dock), and I’m seeing this in 20.04.
It’s possible that this isn’t actually a snap issue – maybe updating any application would cause this – but I suspect that it’s caused because an update to a snapped app will change the executable’s path (and maybe the desktop file’s path) because the path has a version number in it. Maybe the Dock or BAMF or whatever could be taught to look at snap things via the .../current symlink which wouldn’t change?
which is sadly still an experimental feature so you need to explicitly enable it (as described in that thread). then it will make sure that apps are not updated underneath a running instance … instead it pops up a desktop notification asking you to please close the app and update it … not sure where on the road map it is to be finalized and to be not experimental anymore …