When I pull levers to warp from place to place I sometimes end up over objects that I shouldn't normally be over such as boxes or enemies.
Soooort of a bug. I mean, if you use a teleport spell that's what happens, it's only the core teleport spells generally are blinks or specifically requires a space to be empty. Take SwiftStriker though, for example. You can use quickstep to move into occupied squares whether occupied by an enemy or otherwise. Reason why it is sort of a bug is because I'm not sure how this should be fixed. Perhaps a position swap, or even a telefrag.
I like the telefrag idea. But I would say that teleportation must be to an empty tile or a tile with only loot on it. A simple check to see what is there in the programming before completing the spell should take care of this.