I reproduced the bug regarding the guard "multiplying". It's not actually the case...what's happening is that when the guard is in flee mode and the player has him backed up against a wall, the AI freaks out and changes direction every frame. I'll fix this behavior, but I'm going to remove it from the issues because it isn't really a bug.
I've confirmed the bug where you get pushed through walls. It occurs when you land on top of an enemy when they're almost touching the wall. Skeletons are too tall to jump over, though, so I don't know how that particular case happened.
I wonder if the wrong platform is getting removed in tower_01 when playing as the Mage. It would explain why the gate collision is still there while the upper platforms are not colliding.
A good number of those bugs are probably to do with the new enemy code. I recognize the one where the enemies would be jumpy as they move, although that's probably in the physics engine since that can also happen with the player.
Good catch on the bug with vertical platforms. My platform check code doesn't factor in rotation.