When A.M. is shot by Reacher, his coat is fully buttoned, but in the next shot, when the whole squad is shooting him, it's unbuttoned and fully open.
When Neagley is using an AR, picking off guards outside the bad-guy stronghold, her shots are portrayed as highly suppressed although she clearly doesn't have the equipment mounted on the weapon.
Towards the end of the episode, when the crew goes to a restaurant to get breakfast, two buses of MiWay, the transit system of Mississauga, Ontario, Canada, can be seen driving by in the background. They're supposedly in New York.
An eyeball in a jar wouldn't fool a modern bio-metric scanner. They read patterns in the blood vessels of the retina which break down on death. No external preservative would prevent this.
You wouldn't be able to hear the kids radio inside the factory. It was shown earlier that the perimeter fence was hundreds of yards from the building.
In the factory scene there are 15-16 fully loaded 42U racks. There would be a huge amount of noise coming from them yet the room is silent.