You're not running into a height limit, you're running into a falling limit. When the player (or other actors, I think) fall for long enough, the engine teleports them up to a hopefully safe place, so they won't fall forever (they'd eventually hit the bottom limit, which would probably result in Undefined Behavior).
To fix it, just make it so they can't fall so far in a shot, add something they'll land on every 10/20 feet (small ridges they can't stand on, but will land on enough to reset the falling time counter).