I recently discussed such a topic in regards to crested geckos. It turns out that it was just normal pigment. Is this possibly the case with your snakes? Since they are otherwise doing fine, I would inspect them closely, but carefully, to be sure that the dark spots aren't open sores, raised bumps, necrotic tissue or anything other than normal scalation. You should be able to do this with the snake just sitting next to the glass. If no abnormal findings are found, then I would consider it normal colouration until you are given reason to think otherwise.

Ian

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