Plot hole: Nile checks the gun Andy gave her and realises it's empty, which in turn leads her to realise that Booker was setting them up, because he gave that gun to Andy in the first place. No way that Nile, a marine, and Andy, a timeless warrior, somehow both missed the noticeable difference in weight between a fully loaded pistol and an empty one.
Deliberate mistake: The immortals retrieve firearms from the truck and arm themselves, however they do not take any spare magazines. A handgun's average magazine capacity is 15 +1 rounds, that can be emptied in 2 seconds in rapid fire, Jerry Miculek fired 27 rounds from a 1911 in 3.5 seconds; he's a world record holder but still this gives some perspective on how fast ammunition depletes. (01:18:45 - 01:19:20)
Continuity mistake: After the initial attack on the church we seek camera shots of the interior as if Copley has access to CCTV images of the interior (rather than helmet cams), but Copley does not see anything that happens in the room again. The last soldier killed at the church gives a signal to the soldier behind him, but there is nobody following him.
Continuity mistake: When driving the silver Audi A6 the first time, the version they are driving is a diesel, seen by the exhaust pipes facing down towards the ground with a bend. In the next shot they are driving the petrol version of the same A6, seen by the exhaust pipes holes facing directly out from the car. (01:18:33)
Plot hole: The two immortals get captured, they take out all the guards inside the transport van, but they don't break free of their thin zip-tie's which aren't even handcuffs, and they don't fight the ground team waiting for their arrival. It doesn't make sense why they board the plane and don't fight Copley and his team of mercenaries or soldiers. They survive gunshots, and all that's pointed at them is traditional firearms. So the logic here? (00:59:34 - 01:01:00)