I found a game breaking bug that prevents npc's from spawning inside boarded or landed spaceships. Ships that have landed no longer open the landing bays and are empty inside as well as any ships you board are empty. This even prevents starborn from spawning and strangely enough allows players to enter and steal their landed spacecrafts.
I believe this bug is caused by the "kill all npcs on ship or leave ship" misc quest not properly finishing and thus breaking the current save-file. earlier save-files will not be affected and starting another newgame+ instance will also fix this. But once a save is affected by this bug it appears to be broken forever. I do not know exactly how to replicate this bug.
1.10.0 (since launch)
English (EN)
No
Boarding enemy ships. May have been initiated by a vanguard misc mission or one of the early crimson fleet quests that has you board a trade vessel to kill someone. But wouldn't know for sure as it seems random.