DaveTheCoder In clicked control, it says that the VBoxContainer was clicked when you click on the top button, no matter what order they are in, and when I add a third button the same thing happens for all three of them.
TextureButton just not doing anything?
Camp when I add a third button the same thing happens for all three of them.
With three buttons, none of them work, but with two buttons, only the bottom one works?
DaveTheCoder I found out the issue. The VboxContainer that was coming up in clicked control was in the UI of the game, not in the pause screen. I fixed the issue by making it smaller.
Camp it says that the VBoxContainer that the buttons are in was clicked
So that was a lie? 
DaveTheCoder yea, I didn't really read the whole node path, I just read the end and assumed, which was dumb on my part.