Continuity mistake: In the scene where Marcus finds Blair hanging from the power tower, it shows a dark tan stripe around her eyes, but in the following shots it is much lighter and less dark than the previous seconds. (00:47:00 - 00:48:00)
Continuity mistake: When Marcus was freed by Blair and they are trying to escape through the shaft, Barnes shoots a rocket at them. Marcus lies on top of Blair as the fire goes through the shaft, but you can see that Blair's hair is sticking out from under Marcus. When they get up, Blair's hair is not burnt at all. (01:06:40)
Continuity mistake: In the scene where Blair escapes with Marcus and Barnes launches an explosive into the tunnel, Marcus hops onto Blair to save her from the scorching flames. After the fire, Marcus' coat would have been burnt to a crisp, his hair singed off and the skin on his back fried. More evidence pointing to this was that his coat was merely one previously worn by a Resistance fighter, not special in any way, and he has regular skin and hair. (01:06:50)
Continuity mistake: John Connor, whilst battling the T-800, fires a shot into a wall to create an opening. Star jumps through the hole to the left, Kyle jumps to the right, and John jumps through the centre, yet in the next shot Kyle has landed in the centre and John has landed on the right. (01:27:35)
Continuity mistake: Just after Marcus rips out his chip and throws the stool, he jumps to the lower level. As he walks up to the resistance soldier on the MRI table, if you look at the top edge of the screen, you can see that the awning is all damaged from being shot by the terminator that Kyle stabs in the neck. However, the scene where this occurs happens about a minute after Marcus jumps to the lower level. (01:32:55)
Continuity mistake: When John Connor is carried to the helicopter, we can see the older lady Virginia in the helicopter. After the helicopter becomes airborne, Virginia is not seen again. (01:41:10 - 01:41:50)
Continuity mistake: This is right after Conner jumps down to the lower level to get to the grenade launcher and hurts his shoulder. He is crawling away from the T-800 and the shot is from right behind Conner's head. The T-800 is practically right on top of John, but when he shoots the oven and the molten steel lands on the T-800, the shot shows John like 30 feet away. (01:41:15)
Continuity mistake: At the start Connor jumps in a helicopter and takes off, at which point it gets shot down. When it crashes upside down he undoes the lap belt and falls out of the seat, problem is he never did the belt up in the first place and he was wrestling with the controls, so he couldn't do it up when crashing.
Continuity mistake: While John Connor is above the small lake in a helicopter searching for Marcus, he and his crew are attacked by snake-like robotic arms that rise up from the water. The arms partially penetrate the cockpit but in brief, subsequent shots of chopper, the arms, which should be extending from the exterior, are nowhere to be seen.
Chosen answer: It was a strike by Skynet on the attacked facility to try and deny the resistance information and anything useful.
GalahadFairlight