Firet two are the same coin, last one is another, how it originally looked. I've read that this can happen sometimes and is natural. They are all sealed in saflips. The oroginal holders had holes in them.
Proof nickels can and do tone sometimes. It's hard to tell from your photos but some of the darker spots look a little worrisome but it may just be the lighting.
Depending upon the storage environment (shoe box, old shoe, belfry, watch tower) stuff (coins) is gonna oxidize.
Correct proof Jeffs can tone, spot,carbon spot, etc...nickels in general tend to have a higher frequency of carbon spots. I've have slabbed raw unc. Buffalo nickels to have them spot with carbon. There's nothing you can do ...to stop or fix.
I don't think she has ever used the oven for anything but a Laboratory for her burnt food recipes (well, I think it started as food...)