I assume it is a thermal evaporation. It could be a couple of things, my guess is that temperature is playing an important role. I don't know parameters of your evaporation process and I am not expert of your material, but heating the sample could be an issue. This is really easy to check, just do the evaporation process by steps with enough time in between to avoid heating the sample too much. Let's see what other expertise's thing about other possible reasons. 

By Au evaporation, I assume you mean evaporation of Au electrodes onto the top surface of the cells? As Jorge says, a likely possibility is that the evaporation causes heating of the whole cell surface, which causes chemical changes accounting for the discolouration.

Another possibility is that the evaporation environment is not clean enough - i.e. contaminants may be deposited during the evaporation step. Contamination could be reduced by:

-Ensuring that the pressure in the evaporation chamber is low enough before deposition takes place.

-Heating the evaporation source without a target present (or with a shield between source and target) to remove contaminants before carrying out evaporation.

Alternatively, the Au deposition may not be precise enough, i.e. some Au may be deposited on the surface outside the areas where you want to form the electrodes.This might occur because the mask (or other mechanism) used to restrict Au evaporation to the desired areas is not precisely aligned and held in place.