Newer version of Bottles as Executable/Shortcut functionality broken. Appears related to an update dependency and not Bottles. Here’s a quick fix:
sudo flatpak update --commit=779ddf6a44999c6e231aef3b4ffb53d0625ef7af8a0d98a909a9e19e235ed761 com.usebottles.bottles
It definitely works for exe’s. Should work for shortcuts.
Optionally, also choose your preferred downgrade version by selecting a commit from the list after running command:
flatpak remote-info --log flathub com.usebottles.bottles