This occurred on our Survival Saturday Series server and I have access to the host/owner if more information is needed or we need to pull logs. -> {F4432}
First occurrence, Trade Station. The original trade guild on our server was accidentally deleted on the first Saturday of the series, it was remade but no longer declares hostilities or sends fleets. There are no shops except the starting shop at spawn, so restocking is not an issue. I was attempting to cut into a Trade Station with a torch, but the station was invulnerable in a sector with no peace or protection flags (maybe this is normal?). I began cutting into one of its turrets with the torch, obviously not protected, the turret did not like this and mysteriously managed to kill me once I was inside of it. Upon return to the sector, the station had become a red platform, but all of the turrets remained (now undocked) and still factioned.
Second occurrence, Pirate Station(s). Our faction deployed a station blueprint with Pirate Stations in 3 adjacent sectors in order to draw in constant waves of the enemy for farming resources. It was a great success until we warped back to our original sector to bring back supplies in a jump ship (it was deemed the warp gate was not a good idea to use with a lot of supplies given that it dumps you a ways out and there was so much enemy fire). Upon return to the sector, all three pirate stations had become red platforms which were still factioned to [Pirates], but no longer hostile. All of the associated turrets were ejected and now neutral with no faction affiliation.
Apologies if this issue is known and I missed it or if this is something as simple as the server not allowing old docks and I missed it.
Let me know if you need more information, I also have access to this server during the week (different world and slightly different config), believe I may be able to reproduce this and that it is potentially related to sector unload/load.