Had the same thing happen. Had to do the boss again, but got an extra tech card.The game's been crashing quite a few times. First when my friend and I got near the first boss, then again when I put the crystals in the ship.
EDIT: Oh good. The quest didn't count and the crystals are gone because it crashed during the little bunny fixing gif. Guess I have to do the mining mission for a fourth time.
Wonder why they went with putting a gateway in every solar system instead of just having it as a teleport option. They're all identical, right?