It does, i've seen missions where freaky things happen if two ships are docking at the same time. However, and this is especially true for a fleet station, you could just START the mission with everything docked, and have things undock during the mission. You really wouldn't need to have ships docking during a fight, and if all else fails if you just give the ship a waypoint that snuggles it up against the station, is it really going to be a visible difference? anything larger than an argo isn't going to bother docking with a station anyway, usually. Its so much easier to just use shuttles for moving things around.