(Note: This is based on looking at the DOA4 pcb I have here; if there’s been any changes from that to the EX2 pcb, I’m not aware of them.)
It doesnt use a real ground, but you knew that. When you said the ground trace, I’m assuming we’re talking about the same thing; each button has one leg that goes to the end of a diode, and the other end that is rather ground-ish. On the B button, its the trace and hole closest to the USB cable. That same ground-ish line is shared with the Y and RT buttons. I can’t give you anything more specific to go on without seeing what damage or repair you did to the trace, but yeah, if you muffed up something with that line in the wrong spot, it would affect the Y and RT buttons.
The good news is that it is almost certainly repairable. If you need help, post up some scans or QUALITY pictures of the board showing the damage and the repair you made, and I’ll try to find spots you can use for rerouting, but it sounds like you’re capable enough to do that yourself.