Why do you need a ship to "dock" inside the bay? It is only used by ships that dock (by going inside) with the station. If you want them to do that, then go in to the ships editor and give the ship a departure cue. And, instead of hyperspace, change the departure "location" to B5 from the drop-down menu.
If you want a "fake" docking so that the ship enters the bay and then comes back out during the mission, you can't do that. But you can have another ship with a slightly different name (with a extra space in the name or something) and predent its the same ship.