I had a borrowed horse that was a stomper. He was a real fly magnet and he stomped constantly whether he had a fly on him or not. He also came with cracked front feet from the stomping which did not resolve very well. Fly wraps helped some with the stomping.
I also have a horse that I own that stomps, but not as bad as the other one. She was doing some really strange things with her hind legs and I thought “Oh no - does she have shivers?” Nope - this was summer time behavior and she was scratching the inside of one hind leg with the other leg. She tends to have itchy legs when the grass in the pasture gets tall, especially if it stays wet. I am in central Alabama so this is kind of hard to avoid and my pasture mower is not always available. So it may be due to insects or even wet grass/weeds in the pasture.