You need to make an effort to improve enemy pathing so that enemies don’t take as many vertical shortcuts, ideally none. Teleporting through the magical door network is one thing because it happens out of sight and players can hear the doors open and close which gives them a fair indication of enemy movement. But vertical drops always surprise me because they are so illogical. I (and the entire team) often turn away from areas of the map that should be clear of enemies, only to get hit in the back. No one expects enemies to just fall down 30+ft vertical drops because that’s just stupid, but they do it anyway and don’t break their legs in the process. What’s worse is that they often do this in complete silence, so it’s like having enemies warp in through magical star trek teleporters and the player is given no indication that anything is happening.
What to do about this? Well in short enemies should be limited to the same terrain that the players can traverse without damage. If enemies want to move vertically they should be limited to ladders or “steps” that are no more than 8ft at a time. Long vertical drops should only be used as a very last resort and they should impose fall damage on enemies that use them. Big “superman leaps” where enemies jump UP through those same drop paths should be eliminated entirely.
You could make a few exceptions here and there as long as they make sense. For instance mutants are really tough and I don’t think they care much about fall damage, but a poxburster that falls too far should just splat on impact. If you want enemies to be able to traverse downwards then put a ladder in that location with the bottom part removed, this allows enemies to climb within a reasonable falling distance, but not allow them or the players to use that route to move upwards.