Revealing mistake: On each of Sky Captain's hangar doors, the windows are broken in the exact same places, indicating the same window rendering was simply duplicated to make the others. (00:16:45)
Revealing mistake: When the robots breaks the walls of the room where Dex is, there is a lot of debris that fall on the floor. A big piece of debris in the middle of the screen passes through another.
Revealing mistake: In the final scene when the escape pods land in the water, it's visible that the splash consists of large drops, which would never appear in normal conditions but is easier to do as a digital effect.
Chosen answer: About 95% is CGI. The only real part of the movie was the actors themselves (and small objects they handle), with the exception of Dr. Totenkopf, portrayed using archive footage of Laurence Olivier. Everything else was CGI.
Guy