Unable to downloads updates

Hello there,

Two questions, unrelated, but trying not to spam too much.

I did the zypper dup and well, I think everything went pretty well, despite many messages telling me that x. y or z wasn’t installed/updated due to something missing. But the system is running fine.
Except that I’ve lost the App Indicators on the top right (running Gnome) and I noticed that most of the Gnome extensions are listed as incompatible with the installed version.

And I had to reinstall Skype because it wasn’t working any longer. And there’s the question:

I installed most apps via flatpak, and I always have the message “Unable to downloads updates: you do not have permission to install software”
How can I fix this? Is it that I need to add my user to a specific group?

And I did perform the update after changing my PCI Wi-Fi card, from a Broadcom chipset to an Intel Chipset (Model: “Intel Wi-Fi 6 AX200NGW”) The card runs very fine. But I did not remove the Broadcom drivers installed previously. It’s fine, it’s running as expected, but should I still remove the Broadcom stuff via Yast Software management?