I regularly find inconsistency between the "software updates" tool that displays updates in the system tray, and the command-line 'dnf' tool. For example, right now the 'software updates' tool informs me of one available update, but then running `dnf update` in a terminal informs me about "Nothing to do."
Since dnf maintains its own cache, you may be seeing this discrepancy due to the dnf cache not being up-to-date. Running "dnf update --refresh" will refresh the cache before resolving the updates so you should then see the same list of updates as the software updates tool (packagekit). I'm closing this now. If you continue seeing this issue even when using the --refresh option, please feel free to reopen it.