When MacGyver runs to jump onto the Jeep's hood, the Jeep is ahead of him and he's clearly running to catch up, yet he then immediately launches himself from the side onto the hood. It would have been impossible for him to have got ahead of the Jeep on foot within seconds.
When Macgyver and Marietta get to the command center and he unties her then jumps out of the jeep he has his boots on. He was driving and holding onto her. He had no time to stop and put them on.
The gas cylinders beside the missile are stenciled Liquid Nitrogen. These are standard gas cylinders not cryogenic tanks needed to store the super cold liquid.