I believe those marks are from where the marbles came into contact with others during manufacturing process.
Put a handful of marbles onto a flat surface. Push them together. Notice where they touch.
Let's see a picture! The consensus seems to have been that it was a coincidence of how the marbles happened to clink together when they were being made, but if yours is similar, maybe it wasn't just a coincidence...
Bennington marbles are a type of glazed clay marble. They are not very dense. The marbles are fired clay with a salt glaze on them. Benningtons are readily identifiable by both their coloring and the little 'eyes' that they have on them.These are spots where the marbles were touching each other while they were being fired, resulting in those spots being uncolored and unglazed. The term 'bennington' is actually a misnomer. There is no evidence that they were ever made in Bennington, Vermont, or that they have any lineage to the Bennington pottery that they resemble and from which they get their name. It appears that all Bennington marbles were imported from Germany.
Thanks for the help! I figured that was what caused them. I just have to wonder, what are the chances that on TWO marbles, the spots are arranged like that?