The standees replace the miniatures. Each counter represents the “landed” standee/miniature. And you only need 1 per standee/miniature. The stacks in the photo are all duplicates and don’t include one other complete set of counters. So they were provided by accident I assume.
The extra markers are there in purpose of hexagonal bases for cardboard pieces (if they are used and assembled that way). We had ran out of red and blue hexes at one point, therefore some of you have got "H" and "L" markers instead.