I can't say it is necessarily applicable to this species or genus, but Arothron sp. pufferfishes will get dark spots, patches, and/or lines in response to degraded water quality or irritation--sometimes after the fact. I've also seen this happen for no apparent reason and take a very, very long time to go away. Unfortunately, I can't offer a solid explanation or cure, other than make sure that additives are minimal (for risk of irritating sensitive tissues), water quality is as high as possible, and the puffer feeds well.