Strange…
Same Problem here,
flatpak uninstall --unused said it removed them but Pamac still showed them while pacman did notflatpak uninstall --unused said theres nothing to doEDIT:
The Theme was a Greybird and I am on XFCE.
Pamac did not show it, only this KDE- and Gnome-Stuff
I just tried it, but it makes no difference.
Thanks, that helped me… I installed bauh, it showed 6 udpates (in pamac where 2, in sudo flatpak upgrade 0). I applied the upgrades, and now pamac says i don’t have any update left.
But… strange behaviour.
Thanks
Ha…that’s unbelievable. I had done the flatpak uninstall --unused earlier today, so I installed bauh, which I never heard of before, from AUR, and it wanted to upgrade a Matcha theme, which it did…and tada…now pamac-manager does not shows any flatpak updates any more. Thanks SvenB.
I’m not sure whether that works all other affected users, but it seems to be the solution.
Thank you! Bauh helped me too by upgrading Matcha-something and three other packages. 
Pamac just showed today a few brand new updates for pamac manager and for flatpak manager.
I hoppe this problem is solved now with this new updates.
I had this problem with five Flatpak packages. Running:
flatpak uninstall --unused
And then:
flatpak update
Fixed it for me.
Thanks a lot - that did it for me too!!!
I was also getting this update notification for a few days now, but running an update in Pamac UI wasn’t doing anything for it. Running flatpak update just installed the update for org.kde.Platform and finally solved the problem—the update is now gone from Pamac and it says everything is up to date.
One thing that is confusing here is that Pamac did indeed see that an update is available, but it was unable to perform the update.
I had the same issue -thanks to your recommendation to simply run
flatpak update
it’s solved. Thanks a lot!
I updated in pamac GUI, but i also had enabled Flatpaks in there. I had a few days no updates… but today this flatpaks appeared again… there is a serious bug going on!
Maybe it’s just another version of it? I find the Flatpak integration somewhat lacking in Manjaro, sadly. I had MEGAsync installed using Flatpak as well and it broke after one of the recent updates. I reinstalled from the repos and I hope it will be better.
Please create a post in Feedback with details if you would like to share your experience and suggestions for improvement. 
Did you report the issue upstream?
This gets a bit annoying. The KDE and other stuff constantly reappears.
Just uninstalled the only four Flatpaks i had and afterwards did a
“flatpak uninstall --unused”
and got this
These runtimes in installation 'system' are pinned and won't be removed; see flatpak-pin(1):
runtime/org.gtk.Gtk3theme.Greybird-dark/x86_64/3.22
ID Branch Op
1. [-] org.freedesktop.Platform.Compat.i386 20.08 r
2. [-] org.freedesktop.Platform.GL.default 20.08 r
3. [-] org.freedesktop.Platform.GL.default 21.08 r
4. [-] org.freedesktop.Platform.GL32.default 20.08 r
5. [-] org.freedesktop.Platform.VAAPI.Intel 20.08 r
6. [-] org.freedesktop.Platform.VAAPI.Intel 21.08 r
7. [-] org.freedesktop.Platform.openh264 2.0 r
8. [-] org.freedesktop.Platform 20.08 r
9. [-] org.freedesktop.Platform.Locale 20.08 r
10. [-] org.freedesktop.Platform 21.08 r
11. [-] org.freedesktop.Platform.Locale 21.08 r
12. [-] org.gnome.Platform 41 r
13. [-] org.gnome.Platform.Locale 41 r
14. [-] org.kde.KStyle.Adwaita 5.15 r
15. [-] org.kde.KStyle.Adwaita 5.15-21.08 r
16. [-] org.kde.Platform 5.15 r
17. [-] org.kde.Platform.Locale 5.15 r
18. [-] org.kde.Platform 5.15-21.08 r
19. [-] org.kde.Platform.Locale 5.15-21.08 r
the Greybrd-Theme isnt even a Flatpak and I thought the Flatpaks were kind of seperate Containers without any interconnection anyhow.
This actually fixed it for me! Thanks!
I still get this org.freedesktop.platform Updates every 7-14days.
I have no clue why i have this updates, im only installed a single flatpak game.
Edit:
After the update im always use:
flatpak uninstall --unused
I used this command countles times.