The first time they show defcon, they take it from 5 to 4. Five is on the LEFT side, and 1 is on the right. Next time that they show this, 5 is on the RIGHT, and 1 is on the LEFT
There seem to be several 'DEFCON' indicators used at Norad, so we could be looking at a different indicator. An alternative explanation is that we are seeing the same indicator, but from the other side.
The CiscoKid is right. Listen to the commentary on the DVD. They found out afterwards that they got the defense condition order wrong. They admit that they just guessed. Defcon 1 is peace, not war. Although, since they didn't actually KNOW which way defcon runs, this is more of an incorrect guess than a slip-up, not that it doesn't belong here, just defending the movie-makers a bit.