Quicknote

Set env variable correctly.

Here is one example.

flatpak run --env=GTK_IM_MODULE=ibus org.telegram.desktop

Here is another example. This looks like a permanent fix to me.

sudo flatpak override --system --env=GTK_IM_MODULE=ibus

Other possible variables, Showing ~/.bashrc format just adapt like above example

#export GTK_IM_MODULE=$im 
#export QT_IM_MODULE=$im 
#export XMODIFIERS=@im=$im 
#export INPUT_METHOD=$im 
#export SDL_IM_MODULE=$im

Credits

https://github.com/flatpak/flatpak/issues/1671#issuecomment-437288456