has he gotten new shoes lately? When shoeing a horse you file the hoof and it turns white. The farrier might have thought his frog was a little long and needed to be shaved down a bit, or something along those lines...
My dad is a farrier, and sometimes he will trim a frog that looks as if it is long and gets irritated when walking.
About the holes... at this point I wouldn't worry about them.
Try pressing on the holes, if they seem to hurt him, maybe it is stone bruise that indented his foot?
You can tell a gelding, you can ask a mare, but you must discuss it with a stallion.