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.