I’ve not been able to find a report of this issue in the Ubuntu or Gnome bug reports, but apps like pymol which have low resolution icons are no longer being scaled. This results in the Show Apps or the Dock displaying a black square with a miniature copy of the icon in its center. This issue has also been reported on Reddit by Arch users on Gnome 48.
https://www.reddit.com/r/gnome/comments/1jks76v/inconsistent_app_icon_sizes_since_updating_to/?sort=old#lightbox
I opened a launchpad bug against gnome-shell for this bug.
gnome-shell 48 doesn’t scale up low resolution icons like pymol
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Fedora 42 doesn’t exhibit this issue but they have an entirely different icon for pymol.
Broken icon scaling rendering from current Ubuntu 25.04.
Expected icon scaling rendering from Ubuntu 24.04.2
Fortunately, the change from gnome-shell 48.1 https://gitlab.gnome.org/GNOME/gnome-shell/-/merge_requests/3680 eliminates the breakage in scaling low resolution icons when applied to the current 48.0 packaging.
