Well, since you didn't mention where this is happening, I'm guessing this has to to with Schedule CA line 37 columns B & C and how they get to Form 540 lines 14 & 16. When line 37 column B is negative the Schedule CA line 37 instructions say to enter it as a positive number on Form 540 line 16. If the Addition column C is positive then those two get added together and put in 540 line 16.
It's the reverse if line 37 column C is negative - that goes to 540 line 14.
The arithmetic always works out right.
This is all because the Calif FTB doesn't want negative numbers in Form 540 lines 14 & 16.