Other mistake: When Marcus, Kyle and Star are at the petrol station, a flying HK and the giant Harvester robot are able to appear just outside without making any kind of sound. In every other scene of the Harvester and the HKs however, they both make an incredible amount of noise. (00:37:40)
Other mistake: A spelling mistake in the credits lists Diego Lopez as a "soilder" instead of the intended soldier. (01:27:45)
Other mistake: The T-800 manufacturing facility cannot seem to decide just how the T-800's are assembled. When John, Kyle and Star jump through the hole and land amongst a load of T-800 skulls, all of the skulls have eyes that are lit up, and the lower jaws already attached. However, in the next shot when we see the T-800's being assembled on the production line, eyes are inserted separately and are not lit up, and the the lower jaws are only attached at that point, not before.
Answer: Perhaps, but once the submarine captain learns that John Connor has just jumped off the helicopter, what is he supposed to do? Let John drown? John must have known the Captain would have little choice but to pick John up.
XIII