About 15 or so years ago I had a similar problem with some color film I was shooting. There were a number of spots on the film that I thought were caused by the processing, and subsequently gave (and I might add unjustly so) a first rate hard time to the poor soul at the photo lab.
The spots bothered me because the photos were something special, and couldn't be repeated. For about three month I agonized over this problem and probably left the girl at the photo lab with a complex.
One afternoon I was talking to a friend who had been in the business of photography from the time of Moses and he took a look at them. After VERY careful examination, he came back to me and said..."your out of luck, it's Kodaks fault."
When I asked, he pointed out that on the image, (400 speed film) you cold make out the grain patterns. (Keep in mind that on color the silver halide washes away, but leaves a trace pattern.)
Upon inspection, he saw a deviation in the grain structure, color, tonality, etc, wherever the spot occurred.
Simple translation; Manufacturing defects.
It is more common than you think, and I later learned that most people who work on an assembly line, are there for the money... Not quality. So what ever passes, passes.
This is true for just about anything.