I once created a couple small holes in a pinwheel quilt. Three times my needle broke while machine quilting and I finally figured out that it was when the needle hit the pinwheel right in the middle where the points all came together. I marked my little holes with a marker and finished quilting making sure I avoided those thick centers. Then I put a drop of fray check on the small holes so they wouldn't get bigger when the quilt was used and washed. I looked for the holes again after washing the quilt and couldn't even find them!! So depending on the size of your hole, this could be another solution.