The biggest plot hole for me was that Spoiler: Shaw decided to fly to another planet on an alien ship with none of the food, water, basic needs required to survive a trip longer than a couple of days. What was she going to do, wing it by trying to eat the aliens?

They should start the sequel by having Shaw die of starvation in the first 10 minutes.

Unless she was going to hide out in the engineer's hypersleep pod thingie. Even so, it's fucking stupid.