Like AndyP said, I'd like you to elaborate on what "can't use them" means specifically.
Personally, I've never had any problems accessing any of my ships on any server or in SP. They have always worked for me, no matter if they were actually built on the server, or spawned from a blueprint. Likewise, they have always worked, regardless of the faction they were spawned in or built into. The only thing that could plausibly stop a ship from being used under normal gameplay conditions is that it is incorrectly factioned, end as such cannot be used.
A few pointers on Factioning:
- Check your faction module settings, always faction your ships and builds on MP servers (this prevents them from being factioned by other players, or stolen easily if left unattended).
- If you don't want anyone else in your faction using your ships set them as Personal ships (Access faction module, set permissions to "P").
- If spawning your ship or laying down a core, make sure that it is either factioned to your own faction, or unfactioned (there is a checkmark in the spawn dialog for this purpose). If it's not factioned at all, refer to my first pointer about factioning, either fix your faction module settings, or slap on a faction module if it doesn't have one.
The only time's I've experienced ships or anything else not working in SM, is when there is a major lag spike or connection problems on a server. This can prevent just about any player action not registering, and it disrupts rail mechanics and logic functions as well.