When the life raft is open over the hole in the plane it has a cut in it which disappears in the next shot.
Just before Coulson takes a sip from the blue slushy, you can see that his tongue is already blue from previous takes of that shot.
At 04:24 Skye is looking out one of the Bus windows and several raised rivets can be seen. Modern aircraft use only flat rivets in order to reduce drag.
At 15:14 Fitz starts to explain the hydra weapon to the team and says "it's full of lethal amounts of gamma radiation". Since radiation has no mass it cannot "fill" anything. He could have said "it's full of radiation-emitting material" and been correct.