You can try with: rm -r ~/.var/app/app-to-remove. I.g.:
rm -r ~/.var/app/com.usebottles.bottlesFlatpak bad installation
It could happen that a flatpak installation, from a link, goes bad and from a GUI you can’t fix the problem. In this case you can try with: sudo flatpak repair in a terminal.
At least, this was my experience with Bottles.