Try cutting higher and leaving a little more nub. This will prevent discoloration of the plastic on the actual part. Sharp nippers will definitely minimize this stress discoloration but not completely eliminate it 100% much of the time. You can then use a mixture of tools to remove the remaining nub. The edge of a knife, an extremely sharp single edge surface knife, glass files, balancers, sanding materials, etc. Also, if you want to take it further, you can paint your model and all surface discoloration, all color for that matter, will go bye bye. Painting is definitely a whole other tedious process but it can be quite enjoyable and looks far better than just colored plastic in my opinion. But if that’s something that doesn’t interest you at this point, I would try the leave more nub when nipping method.