I have 4 quarters like that and one nickel. A friend has a proof set with the Nickel having rainbow looking colors. No clue why
The coins can tone even in a proof set. Gases can get trapped in there and tone the metal, or, perhaps it's not 100% air tight. I have an older proof set (30 yrs) and one of the coins has toned, but the toning probably started 15-20 years ago. As for the quarters, (this is an old thread) I am going to assume it is environmental toning. Which usually means the coin is just "rusted" darker. Often times these coins are recovered from the ground via metal detecting and reintroduced to circulation. The air, water, soil, pollutants will react with the metal and turn them very dark. A missing clad layer is very rare, quite noticeable and has an attractive bright copper color on one side. And it will weigh less.