Factual error: San Francisco Bay's deepest spot is 360 feet deep and that is directly under the Golden Gate bridge. Godzilla is only 355 feet. His head would be under water when he stood up in next to the bridge. Also the bay is fairly shallow everywhere else - most parts only reach 45 to 50 feet deep. His dorsal fins alone at 34 to 37 feet tall. So there is no way he swam all the way up to the bridge and then stood up in the water with it only being below his belly. He also couldn't have displaced that much water for it to cover him.
Factual error: When the 6 service members are carrying the warhead to the boat, they hold it with ease. In reality an actual warhead weighs more than 2,400lbs, so that mean they would each be carrying more than 400lbs each with no apparent effort.
Character mistake: All the characters wearing gas masks are wearing them with the straps over the hoods. I was army trained, and you always wear the mask next to the skin for best seal, with the hood over the top.
Factual error: In the scenes on the railroad bridge: (1) the gap between railroad ties varies from 18 inches to 6 inches. Ties on a railroad bridge usually have an 8 inch gap. (2) The muto is stated to be 300 feet tall. In different scenes the muto appears to be taller, shorter and the same height as the railroad bridge. (3) A diesel locomotive averages 60 feet tall which is 1/5 the height of the muto. When the locomotive careens over the end of the bridge, it appears to be much smaller. (4) Railroad flat cars average 60 feet in length making the incomplete nuclear missile on the car almost 50 feet. They are not this large. (5) The railroad bridge appears to be spanning a river but its design is terrible. It would fall down. In the scene with the beached russian sub: the sub is probably a typhoon class which is 500 feet long and 75 feet wide yet the muto towers over it.
Other mistake: In the train rail scene, we see Femuto has eggs inside her pouch, but later in the movie before she lays her eggs, there are no eggs in her pouch.
Answer: Due to the storm, it became difficult for the soldiers to see one another. The flares were used to help them keep track of their positions during the skydive.
Casual Person