Quick repro steps:
Model a hollow box with a 1m x 1m hole in the roof.
Add a 1m x 1m box covering the hole.
Rig the hatch in mlod/model.cfg/config.cpp as a door.
Add planar/3D ladder positioned to exit point of hatch.
Add ladder "start"/"end" named selection vertices in memory LOD relative to the ladder & hatch positioning.
Define - ladders[] = {{"start", "end"}} in config class.
Climb ladder, watch character climb ladder through geometry mesh of the hatch.
Alternatively see Razazel for model I sent him with this exact issue evident in the hatch area that is in the screenshot below.