First one is: Enemy ships seem to be able to hide inside asteroids. You can't shoot them but they can shoot you.
Next: An item for a quest wasn't rewarded
Last: On a random exploration mission where you have to 'collect medical supplies' that some federation vessel lost there: My crew runs straight for these strange rock pillar formations where they are stuck with no way out. Enemies glitch inside of the ground (kinda like the ships in asteroids), and the final supply crate is un-usable, so the mission is un-finishable.