Rust on a die would create a hole or depression in the die, which would in turn create raised patches on the resultant coin.
What's happened here is "spot corrosion". The coin develops a mostly adequate oxide layer that prevents corrosion, but a couple of "holes" in the layer allowed damage to occur when the coin was subsequently placed in a corrosive environment (eg. buried in acidic soil).
The coin was then chemically cleaned, dissolving the corrosion but leaving "pits" where the corrosion used to be.
You can see some before-and-after pics of some very similar damage on a coin I cleaned in this old thread
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