Visible crew/equipment: The boom mic is visible in the bus' windshield when Ben Affleck gets off near the end.
Suggested correction: I think that is actually a reflection of one of the street lights. You can see a very similar street light behind him for a split second as soon as he gets off the bus. They likely would not have used a boom mic in the scene anyway, as there are no speaking lines.
Visible crew/equipment: When Ethan accidentally shoots Peter near the end of the movie, when he says "don't panic" while getting out of the car you can see the camera's shadow on the back of the car.
Visible crew/equipment: When 7375 and 7376 pull out of the siding in the attempt to slow down 777, Judd Stewart is the only engineer controlling to two engines, he is sat in the front engine (7375). However, when the camera is on the second engine, 7376, a person can be shown sat in the cab of 7376.
Visible crew/equipment: When Frank goes to Cooper's office there's a glass-top table and carpet with a striped pattern. After Cooper calls Frank "Grandpa" then kicks him, a few shots later (before Frank lifts the glass-top table) the pink T-mark taped to the striped carpet can be seen, in the underside reflection of the table's glass. (00:53:15)
Visible crew/equipment: When Jarod goes into the basement for the first time, the shadow of what appears to be a suspended microphone can be seen swinging pendulum-style. (00:29:47)
Visible crew/equipment: When Mister and the Boy are keeping watch in the woods, just after Boy asks "What are we going to do when the baby comes?" They heart a noise and stand up, as the camera follows Mister you can see lights in the distance, even though they are supposed to be alone in the mountains. (01:20:00 - 01:21:00)