Docking modules are buggy, so ships that have already been undocked from you stay as "docked" so that the docking module(s) cannot be used. Only fix I've found is to get killed.
When the ship undocks, it will still say its docked in the list. You can then Jetison the guy, and he will be teleported next to your carrier as if he jsut undocked (again).
Another aspect of the bug is that for me, if you jetison teh ship while the player is still online and really docked, he will end up 100k under the sun.
This was a while ago, maybe the bug changed from then.