@nprofile1q... this update system is the smartest one in Linux. You don't want to replace binaries in-place while the system is running. You want to shut down, replace all the files that are updated, and power on
The issue you're describing is not with Fedora, but with GNOME Software, which is and always has been absolutely awful, not showing half of the updates, or updating only some packages, while skipping some, sometimes installing updates unprompted. Just remove GNOME Software and use terminal