That prompt and check box are a result of packagekit seeing pending updates in the metadata used by packagekit and may not match what is seen with dnf (especially when there are updates to flatpaks pending that are not updated by dnf). To clear that out manually you can perform both dnf update --refresh and flatpak update before the shutdown.
You also can turn off the automatic updates to stop that message appearing.
still the same, did all your recommendations
i did sudo dnf offline clean, and fixed the problem
Gnome Software recently switched to using dnf5daemon as backend, which is the same backend used if you run sudo dnf update --offline. Therefore you can use sudo dnf offline clean now.
