So I just did a quick google search and it seems like the solution is to sleep... A lot. I slept 10 times for 12 hours and the NPCs are no longer hostile, but it may require less. Anyway, the problem is fixed.
I accidentally looted something in front of other npcs in Groundbreaker, then ran to my ship. Now, whenever I go onto the ship all of the NPC's are hostile and shoot me on sight. This is pretty gamebreaking, unless I kill all of the NPCs... Which is also game breaking. Help?