The answer's a bit complicated, the short answer is all of the above and I think that may be the problem. It's a station that I've built modularly. It consists of one central ship that has had 3 ships that have been radially docked to it in flight. All three are docked to a non-stock component that has integrated docking ports there are no menu options on this part to allow for undocking, so I think this may be part of the problem. Additionally, one of the 3 ships was built in the VAB as two separate parts connected with two docking ports. I can not undock any of the ports on all of the ships. I'm thinking my best bet is to just start a new station and design it so that all of the ships connect only using stock docking ports.