Nightmare Fuel: When the storm overtakes the Nimitz the first time, there are some eerie scenes of sailors being overwhelmed by the disorienting effects - in particular, the image of a hand being electrocuted by a control panel.
Genius Bonus: At one point, Yelland's XO informs him that the Zeroes are coming straight towards the Nimitz with an armed strike group sitting on the flight deck, at which point Yelland promptly orders the Zeroes shot down. Anyone who knows their WW2 history knows that the Japanese carrier Sōryū was sunk when she was caught in a similar predicament by U.S. warplanes.
They Wasted a Perfectly Good Plot: The plot probably would have been much more interesting had the Nimitz actually intercepted the Japanese fleet, which would have irrevocably changed the course of history for better or worse. Instead, it is stopped at the last second by Deus ex Machina. Showing a 1980's air force taking on a 1941 air force would probably require modern computer graphics to get it right, though - the model budget would have been HUGE.