If I use Pamac GUI for flatpak updates, it’ll go through just fine, and refreshing the updates list will show that there’s nothing pending. However, on the next restart, the same updates will show back up.
If I use the terminal command in Konsole “flatpak update”, it updates fine, and there’s no “reset” of the updates on the next restart.
Yes, this is a known bug.
Well it’s not exactly helping me shake this belief that pretending that I’m a serious hacker when updating my system through the terminal isn’t the best way to use my computer.
That’s for children. Real hackers do it from the tty. 
Real Hackers use Social Engineering, and so don’t need to type anything. They get the Mark to do that for them.
Get used of the terminal, then you will lose the feeling of beeing a hacker pretty fast.
My wife was a typical Windows user. We are using Linux since a few years and it happens more and more often that she’s asking me “Isn’t there a faster solution via terminal for this or that task?”
Sometimes even i have to search. And most of the times i find a better way.