@Jack : I\'ve run into this issue before, what happens is when you purchase the ship and a shop is near a sector border the ship will sometimes spawn in the neighboring sector. To retrieve it go to the sector in the direction of the ship and when you cross it should allow collision with the ship again.
There is just one little problem sometimes with this, if the core is imbetween sectors the ship may become unpilotable, to remidy this use another smaller ship in the sector the ship to be retrieved is in and bump the ship until it is fully in one or the other sectors in order to retrieve it.