Ok I did a bit of googling (I don't use flatpak stuff so its a bit new to me), it seems that software manager will only manage the finding and initial install of flatpaks, you need to do the rest yourself. From terminal try:
flatpak list
Find the entry for Joplin and copy the ApplicationID then run
sudo flatpak update APPLICATIONID
I just grabbed it from here - How to Install and Use Flatpak on Linux - Linux.com - so have a look yourself if you want