Decals are printed in a series of applications when silk screened. An initial film layer, then successive colors, then a clear top layer. Each layer has to be “registered” to the previous ones. Often you can see the “reg” marks at the corners of the sheet. They look like bullseyes.
For instance, a RAF would be a white circle, followed with a blue ring, followed with a red dot.
If the decal printing was out of register, the red dot would possibly not be centered in the blue ring.
A giveaway would be that the bullseyes visibly weren’t directly over each other.
Theres no way to fix it. It’s registered or its not.
I would imagine that digital five color printing is the way of the future, similar to what you can do except for white on an inkjet printer.
Its worth learning which decals are most highly regarded, both for color accuracy and registration.
Cartograph has always been top notch in mass produced kits, Microscale another.