You in effect just left your original ship (OS) in the dock of station unattended, where they have no shipyard and therefore no storage facilities. The galaxy wide tracking system, always knows what your current ship is, so that bounties can be properly applied.
Intra-Astra/Shipyard Facility, isn't just a recall system, it's a registration and authorisation system for ship access. So when you got in your new ship (NS), you are then registered to that ship. One could surmise this is part of an anti-theft system so that only authorised access lets you get to the desired hanger bay. You are in effect illegally parking your OS where you left it.
While I understand your complaint about not being able to access your ship, personally I think from an immersion PoV you should have been fined for abandoning your ship and taking up a docking bay (rather than a storage bay). From a game mechanics point of view, it also makes sense that you could not access your OS, because your current ship authorisation was still set as your NS.
