Britt, Although I've never experienced very dark to blackened boiled peanut shells, I've heard several explanations for this.
Aluminum pots. Aluminum pots blacken when boiling peanuts. Over time this darkening may transfer to the boiled peanuts.
Iodized salt. I've never experienced this myself, but some people say that iodized salt causes blackening of boiled peanuts. This may be hearsay.
Old peanuts. The inner color of peanut shells darkens from yellow, to orange, to brown, to black as the peanuts age. It may be that when this happens you have purchased more mature peanuts. Peanut harvest profile chart.