When Boysie and Iris leave the Colonel's empty office she turns off the lights, but as we see them exit from the other side the room is not dark.
When Frances Ann Chandler gets on the subway car, only the left door closes in a close-up shot before the train starts moving. Then in a longer shot, both doors are closed.
When Oakes is in the back of the lorry looking through the rifle's scope, the perspective of the second time is much lower than the first, yet he hasn't moved.
The bomber on the ground is not the same one shown taking off. The one taking off has a solid colored nose and no fixed probe sticking out, among other differences.
Dialogue refers to "cyanide" and "prussic acid" as separate entities. Prussic acid is hydrogen cyanide.
When Boysie is in the harness shooting at targets, he is using a six-shot revolver, but fires eleven shots without time to reload, or is seen doing so. He then empties the cylinder, is seen reloading two rounds, and then fires off three more shots.