When Lydon and Skye are kissing, Skye takes Lydon's t-shirt off, but the t-shirt is still fully on when they get onto the bed.
Chan's hood keeps changing position on his shoulder, when he's talking to Raina about leaving her.
During the car chase sequence between Agent Coulson and Miles, Miles tries to initiate what he refers to as the "gridlock protocol", he does this by using his cellphone however on the screen a video play list is open, called "Act 1 Video Pla..." and the file he chooses is called "gridlock.mp4", revealing that it is a video file that will subsequently play.
When the team is in Austin. The first shot of Skye and Grant look like they are actually in Austin. Which is green scene shot? But when Grant starts chasing Miles. Fifth Street doesn't look like what was being shown. I think the directors got confused between fifth street and sixth street. So I know for a fact that they didn't shot this scene in Austin. Because none of the buildings that Phil were passing looks a thing like what that area looks like.
Fitzsimmons discuss the fact that Lydon spends a lot of time playing Minecraft, running a rather nasty mob, not just as a pigman, but a zombie pigman. In Minecraft a "mob" is any entity other than a player that moves and acts, and a zombie pigman is a mob, but actually not a very aggressive one. Additionally, it is the only type of Pigman in the game, there is no non-zombie pigman.