Due to their weight and a lower coefficient of friction during braking, loaded trains take incredibly long distances to stop. The distance shown from the explosive to the train- several hundred feet- was too short for the train to have stopped as was shown. A train configured/loaded as shown at the speed shown would take at least a half mile to stop.
Attention on Deck is not called in food service spaces onboard Naval Ships due to the tight spaces on ships. This is observed for even the President of the United States.
At 37 min 39 sec, Captain Chandler refers to the President as the "Commander in Chief" and then gives a horrible salute. He would have identified him as the President of the United States. Moreover, the Navy is not permitted to salute without a cover on.
While it is true that a fully loaded train towing a few dozen cars would take a long distance to stop, well over half a mile, this train was only towing five cars, which were loaded with a very light cargo that didn't weigh much. So considering that the train wasn't towing anywhere near it's normal load it would be able to come to a stop in a much shorter distance.
While observing the food warehouse in "San Diego", the warehouse building is clearly labeled "Port of Los Angeles".
This episode is supposed to take place at Naval Station San Diego. However one of the main buildings clearly says "Port of Los Angeles" on it.
At 36 min and 51 sec, Castillo ordered his security detail to shoot Captain Chandler. It can be seen that 3 warning shots were fired at security details feet. There are 2 problems with his: first, warning shots are not authorized for small arms fire and second, there appears to be 3 ricochets, indicating 3 rounds fired. However, only 2 shots can be heard. Moreover, it is damn near impossible for 3 shots to be fired so quickly and so accurately from a bolt action rifle.