Fedora 41: Cannot open some Flatpak applications

GNOME changed the default graphics renderer twice between F39 and F41: from gl to ngl and then to vulkan. The errors might be related.

Were the Flatpak apps and runtimes upgraded after the system-upgrade? If so, you might want to try a repair wit sudo flatpak repair.

If still having issues, you might want to take a look at this workaround too.