Mananaged to get a -17/200 empty separatist squad. No screenshot. I was bored...
It seems to be happening when you look at the pilot option and give it upgrades, but don't actually select the pilot for you squad. After a few switches it takes away the upgrade values, I think. Not everytime though.
They need to add a subroutine that checks the sum of the saved squad if they don't want to rewrite the running total code...