Turns out the problem was in the player node structure. The pausemenu is a child of a Container. The problem was that said container had a size of 40x40, as shown on the pic below. Simply reducing it to 1x1 or 0x0 fixed the issue.
EDIT: There was also another container, the “gameover” just below the pausemenu, that also had a square size around that same area. So, TLDR: check for any “empty” containers if you get a similar problem.