When the MECH agent electrocutes the people riding on the train, the vehicle continues moving. The train's safety mechanism should have made it stop to a halt shortly after the engine driver passed out.
Optimus Prime stops the speeding train by clinging onto its front, gradually bringing it to a halt. However considering the velocity of the train, and the hardness of Prime's metal hands, the locomotive's front portion should have been crushed during the act. Instead, it looks perfect even after Prime has made it stop.
Just before Starscream gives orders to the Vehicons, his left arm slightly passes into his shoulder armor.
Agent Fowler himself survived the jet crash unscathed, without wearing protective gear or ejecting. The jet itself is also undamaged. Fowler handles the situation as if nothing happened. What's more, even the volatile device he was carrying remained undamaged, though later dialog reveals how fragile it is.
If the "D.N.G.S." is such a dangerous and important military device as the characters claim, then it makes no sense for them to have only a small number of military personnel (one or two) defending it.