Tested on Debian 8.0 64bit, java 1.8, headless server:

• set WORLD = TEST in server.cfg
• only server-database/test was created.

This suggest the issue is only present on singleplayer.

I've noticed the same. These are the same turrets that can't be detached, even if the entire docking mechanism is removed.

That might be a separate issue alltogether.

I have a theory that this has to do with the rotation of the turrets when they're created at the shipyard. I need to do more testing though, but so far it seems that if a turret isn't moved in any way, the shipyard doesn't mess it up.

This is still an issue in the latest stable version.
I created a fairly big ship in a shipyard, then took it out for a test flight. Only the main ship was in the test sector, together with 1 attached part on a rail. All other rail items connected to this part were missing.
Upon return to the base i notice ghostblock remnants of what were the missing parts. Albeit shifted in place. These ghostblocks can't be intereacted with in any way. When the server is rebooted, these ghostblocks materialize in the center of the planet right below the shipyard. (and causing some collision lag as well)