I have also come across this issue. Has anyone else had this issue? I created a shipyard for a class of ship, designed to fit the ship perfectly with lots of room to spare. If I create a design from a blueprint it'll dock. If I unload the same design and re-load it, the ship suddenly now doesn't fit. (so the game says).
EDIT: removing and replacing the yard anchor (in the same spot) fixes it for one use. Adding to bug tracker. I mean the unintended features tracker.