I'm not sure how this bug wasn't fixed yet, I've had it twice so far. Enemies just randomly started to become stunned after every one of my hits. I deleted all the runes out of my swords but that didn't fix the issue. I have runes in my griffin set gear but they aren't stun runes. How do I fix this problem? When I had this before all I had to do was delete my swords runes and it worked, however that didn't fix the problem this time. It totally ruins the game.

Try to verify the the game files through Galaxy (or reinstall the game manually). This fixes a lot of bugs you run into.

P.S. On my first playthrough I noticed I could kill a Leshen by just attacking it constantly. It was just getting staggered by every hit (not stunned) so it couldn't do anything.. I tired it this time but it seems like it was fixed. He'll take a few hits and then teleport regardless of what you're doing.