Not quite a bug, more like evidence that this system needs to have some edges rounded.
When you call a skyship, it's linked with your character. Since it *is* impossible for a character to 'enter' an NPC or an object, the 'skyship' is simply an NPC loaded by the code for show. The actual code that works the skyship goes by what's linked. Most players wouldn't be able to just 'goto' a place and make a landing site, however there probably should be a way to cancel a skyship request.
I'll take a look through the code when I get a moment.