We are a retailer in Ottawa. We sell thousands of square feet of this material per year and this is not uncommon.
I have seen some material do this more than others but it really depends on the vein/deposit the quarry is into.
Whatever you do, do not attempt to clean or remove it with an acid like CLR or Rust Out Etc. This can cause staining of the material and can actually decompose the material.
It is impossible to make anyone responsible for this (I always tell clients "if I was God I would have made the stone perfect"), it is just the nature of the material. I think it contributes to the overall look and is not something anyone will even notice (It is not like the stone is turning purple for example).
I would be happy with what you have there, the installer has done a nice job and the product looks to be a high quality material.