And I bet the bad side was your off hand side?? If right handed, it would be the baits left side if it is facing you OR the bad side was pointed a direction that didn't have good lighting on it.
I don't know if this is your problem, but I have some bad habits when painting. When spraying the back make sure you go the same speed and try to maintain a similar distance over the curve of the back. Start and stop the airbrush only AFTER it has went over the entire length of the bait. If you start, stop, or reverse direction, before clearing the end of the bait the paint will be thicker and that particular spot. If you dont want as much paint say on the top of the head, just paint the back spraying only one direction.
#1 rule: make sure you have good lighting in the paint booth.