Captain America bends one of the truck's two exhaust pipes to spew into the trailer. But in the shot from the front moments later, both exhaust pipes are straight up.
When he is on top of the truck, and the door gets unlocked and he swings it open knocking the two guys down the embankment, a few minutes later the chopper lands on flat ground and the pilot runs right up to the truck as it's parked beside a flat plain, with no embankment in sight.
The view from the front of the truck has the same hill in the background in many shots.
When explaining to Steve how the FLAG serum works, Dr. Mills says that it only worked properly on his father's cells, "cells which have been passed down to you." But this is impossible - only DNA can be passed down to a son from his father.
One of the villains has outfitted his revolver with a suppressor. There is only one revolver that can use a suppressor by design (The Nagant M1895). The revolver the villain used was a Colt
Dr. Mills states that the test rat's body is rejecting the FLAG serum. But this is impossible: human steroids would be chemically similar or identical to rodent steroids - there would be little if any rejection. - The FLAG serum was designed using cells from Steve's dad and so was engineered to work specifically for his genetic structure, which is why they asked Steve to take the serum instead of finding someone else.
When Captain America is trying to stop the truck, he radios in to Dr. Mills to tell him that he had dropped his bike and it needed to be picked up. Moments later, he bends an exhaust pipe to an open vent to make the passenger ill. With the volume that Captain America had to speak into the radio, the passenger should have heard him talking and been able to react to his being there.