After Sterling comes back out of the mayor's hotel room and yells at the FBI agents (approximately at the ten minute mark) they are all outside with the door shut but in the next shot it shows him opening the door to let the FBI agents in.
In the final scene, the tan/orange boom arm of the aerial working platform sitting on the dock appears in several shots as turned, extracted and raised well above the ship's deck, but in the final wide shot (when Nate is lying down) the boom is shown lowered (fully stowed).
When Nate is negotiating the deal in the final scene, it is an obvious green-screen shot, as most of the people are "hovering" above the deck of the ship.