When cruising at 50k feet, there is no smaller aircraft on top, used in episode 14. In a shot later on, it is showing.
During the deduction scene when Agent Coulson was inspecting the pistol magazines and found that 5 bullets were missing from 1 magazine while 1 bullet was missing from the tracer, the reality should have been 7 bullets missing in total because earlier when 'Agent Blake' was changing magazines he needed to reload a new 'tracking' bullet into his weapon.
When Agent Blake is being attacked he reloads after firing 5 shots. The Sig Sauer he is holding holds at a minimum 10 rounds. He also manually racks the slide, indicating that there was at least a bullet left in the chamber. However, he was changing to a different type of ammunition in order to shoot a tracking device into his attacker, as explained later in the same episode.
Obvious stunt double for Blake when Deathlok attacks him and throws him into the wall.
Hydra ordered everyone killed on board the aircraft, except for Coulson.
Yet, when landed the weapons of the aircraft are taken out and right after that the aircraft is being taken under random fire from outside. Negating that order.