I mounted a Deimos Ares cockpit at the front side of my ship and the Taiyo landing bay module underneath, in the most forward position possible (due to geometry reasons, the Taiyo module won't snap to the connection points on the underside of the cockpit, so the most forward position possible is below another module that is connected to the backside of the cockpit). With this combination of modules in place, I ended up jammed underneath the landing bay (completely unable to move, except for fast travelling) whenever I left my ship. This happened repeatably in all landing spots (space ports and planet surfaces).
The problem only went away after replacing either the cockpit or the landing bay with a model of different geometry.