It's very hard to tell which passive nodes are only assigned to a weapon set

Optimally there should be a different color or something that tells us the node is assigned only to a weapon set.

A tooltip would be sort of useful, better than nothing.

What I end up doing is to use the refund button to see which points are gained -.-

Playing on Console UI if that makes a difference.

I agree. This is very confusing, and i guess the best way to solve for this would be color differences. In a perfect world we could designate colors for weapon set 1 vs weapon set 2, and keep the common nodes Yellow.

I am on PC. yet it is still a bit confusing.

Idk about console but there is a color swap that differentiates them already...