It happens quite often on my Linux systems where the Joplin window obscures the dialog.
It does ask for a file. So there is either something wrong with the Flatpak app on your system or the app doesn't like your system configuration.
Do you realise that even though you are using the Joplin forum for support, the Flatpak version is not produced by the Joplin developers? It may be worth finding out who compiles and publishes the Flatpak and raise an issue with them.
Another option is to not use an unofficial third-party version and install the official AppImage.