Revealing mistake: When the Zeros destroy the yacht, mooring lines can be seen holding the boat in place as it explodes. Obviously, it isn't actually at sea, but is very near shore. (00:45:35)
Revealing mistake: When the Marines shoot the Japanese pilot, you can see the wire used to set off the blood bags coming out of his pants leg as he falls. (01:11:30)
Revealing mistake: During the dogfight scenes, they show the pilots of the F-14. In the visor, you can see the reflection of an A-6 instead of an F-14 being used. Turns out, they dressed up some A-6 aviators as F-14 aviators for the shots.
Answer: First, he had a look of concern for the young pilot under his command. Second, he is also confused as to what exactly happened. They believe it was a first strike weapon, that the world was ending.