Blindly dropping complete applications into a folder standardized to hold just .desktop files is begging for breakage.
If you want to install for all users, expand somewhere in /usr/local/ or /usr/share or /opt, then copy just the .desktop file into /usr/share/applications/. Tweak the paths in the copied file so it points where you actually put the complete application.
Similarly, if you want install just for yourself, but have the icon show in the menu properly, expand into a folder in $HOME, then copy just the .desktop file to ~/.local/share/applications. Tweak the copied file for correct paths.