Perhaps not connected to GSX at all, I am sure Umberto will know !!
It's caused by the building crashbox, but I'll need to explain it better:
- Passengers must be configured to walk "on ground" (even if they have an height, it must be above ground), because airports aprons might be sloped, so if passengers didn't follow ground, you would see their feet either slightly raised or into the ground, when they walked along a sloping path, even a very gentle slope would be very visible.
- The building crashboxes are not fully 3d walls, they are more like 2.5D, meaning their roofs are changing the ground altitude.
- The building crashboxes are not always precisely following the exact profile of the building, it depends how the airport is made, but sometimes they are more like bounding boxes that won't match the building profile, so even if you visually see a recessed area like an entry, it might still be inside the larger crashbox, so the ground altitude there is really on the roof.
There might be tricks used by airport profile creators to fool the sim into accepting those waypoints, but they don't always work because it depends how the 3d building is made, so in some cases, the only solution is not placing waypoints in places that might be inside the building crashbox.