After you complete the Human error quest and own Covenant as a settlement, all of the items inside will still be marked as owned, making all of your settlers immediately hostile if anything is taken.
This can be fixed via the console on pc by manually selecting any owned items and using the "setownership" command, making them able to be retrieved without issue.
--------------
These bugs only apply if you have taken the destroy the bunker and attack the town route. !!!
If you have subdued the bunker with the charisma option then the turrets wont target you, and all things may be picked up without mishap.