Very good chance your right. First time I don't really recall what I was near but this last time, I was out from the moonglow docks. Didn't think I was that close though.there are certain areas of the map that are no boat parking zones and there's a good chance you were in one of them and didn't realize it like below magincia
I noticed that but so far, only around the Seamarket.Sounds good. Your ship gets placed away from docks after some time period. Some docks have the bouys, you cant stay inside those.