I bet the most likely cause of the flaws is that they are manufacturing defects (maybe it is about dust or debris in the dies, improper polishing of the dies, or uneven distribution of the planchet material).
Of course, I suppose the flaws are due to die wear. Over time, the dies used to strike coins can become worn, which can cause imperfections in the coins.
And lastly, I don't exclude the post-minting damage. Yup, it is less likely, but still possible, that the flaws are due to post-minting damage (the coin being scratched, or clipped).