Some of the earlier chips had brass filings added to the clay to increase the weight. You are seeing the brass corroding (turning to copper oxide or sulfide). Since they are all through the chip, cleaning probably won't help much.

Later chips used lead dust which doesn't change color as much when exposed to the air.

This is my own explanation. I don't think I've ever seen anyone else publish this as the reason for the freckling of earlier HCE chips.