A well known problem since the days of yore. If you place stairs underneath a floor latch (no matter the orientation), you need to crouch in order to get through. Making the hole a little bit bigger (or the collision box smaller) could help. That, or introducing mildly steeper stairs.
Also, fun story: When you uncrouch too early, before you're completely through, there's a chance that you'll get catapulted quite a long distance, and of course die upon impact. I got catapulted from Levos (D1;H4) to Levos (D1;B4) yesterday. It was fun.