As you select each derelict on the map you'll see MISSIONS in it's list and a completion number. You need to do all encountered missions and contracts within the derelict before completing the mothership. If you're having trouble finding out what mission you still need to complete, make sure to check your mission log, the mercenary hub and thoroughly explore the entire derelict for characters with dialogue. There's a few missions that can be completed a number of ways but it shouldn't be possible to fail any regardless of the outcome.