Unable to Remove FreeCAD

It looks like the Desktop Entry was not removed when Flatpak did the removal.
Can you check:

find / -name '*.desktop' -exec grep -H "Name=FreeCad" {} \; 2>/dev/null
find / -name '*.desktop' -exec grep -H "Name=Minder" {} \; 2>/dev/null
find / -name '*.desktop' -exec grep -H "Name=Scribus" {} \; 2>/dev/null

Remove any leftover Desktop Entries that you find; log out and in to test.

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