A rail docked entity after completing it's movement (at the end of the rail segment) turns into a no-clip part, player falls through the docked entity under influence of main ship gravity module.
Solutions include, going into the core of the docked ship and placing blocks on the no-clipped section, makes the section "solid" again. Other solution is to reverse the part to it's original location, both on the way and at the original location it is always solid.
Only happens after I completely exit the sphere of ship alignment and then return, however it doesn't seem to be easily reproduce-able.