Ensure you apply the colors by name; that is, if a color in the palette is called 'hat', use it only for the regions that compose the character's hat, even if it is the same color as the character's nose.
Use the correctmodel. If you have more than one character in the drawing you are working on, you will also be working with two or more models, one for each character. Don't use colors from one model to paint another character.