So I figured out what the issue is after some detective work and some experimentation. I had the Pop! ppa on my system for some reason. I guess this was a side effect of using the Pop Icon theme. I was searching through folders in /var/lib/ and found an empty pop-upgrade folder. At first I was not certain what it was, but it was entirely too coincidental for me to have a Pop!_OS system upgrade message and run across this folder and not have them be connected.

I have TimeShift on a daily schedule (highly recommend this people) so I decided to just sudo apt-get remove pop-upgrade and see what happened. I did this and then used autoremove but I ran into issues. I no longer had an ability to get to my default Gnome Settings menu. There were probably a bunch of other issues.

So what I did was I used TimeShift to go back to the day before, and when I went to apt-get upgrade I realized that gnome-control-center was being held back from upgrading because it needed additional packages. Those packages were libpop-upgrade and something else. So now I had it cornered. I must have used dist-upgrade earlier that night without realizing it, and it just force installed those extra Pop! packages, which led to the message. After I removed the Pop! ppa from my sources list, gnome-control-center no longer wanted to update, and pop-upgrade was not requesting an install.