Can't reproduce it over here, sorry. Just installed flatpak on a clean 4.0.1 SFOS / XZ2c and it worked as it should.

I presume that you have run flatpak-runner from grid or cmd line without any options. It is needed after installation of the apps to make them appear in the grid. Also it is needed to generate extension.

Maybe, just in case, run flatpak-runner and choose from pulley menu Extension/Update extension