I wouldn't be too concerned then.
The gelding at my barn just gets really itchy from his hives, but as soon as we found out what was causing them, they started going down.. of course as soon as it was time for something else he was allergic to to come out..
So long story short, your girl is probably just allergic to something, so no need to worry unless they ever get much bigger and pus-filled and yucky.. yeah, you get the point. But I highly doubt they will.