Stumps of lost limbs are a result of closing wounds in such a way that the stump is covered by skin. The body doesn’t actually generate new skin – see here for an example: http://www.medicalexhibits.com/obrasky/2008/08082_01X.jpg
I’ll leave the tooth socket to someone else as I don’t think I could explain this properly.
When I’ve had teeth pulled, sometimes the hole was stitched shut, but sometimes it was left alone (I was given a syringe to wash it!) and the surrounding tissue swelled to squeeze the hole away.
(Note that there’s no skin in your mouth, that’s mucous membrane, like lips, nostrils, the inside of eyelids …)
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