These are the larger of the holes in my Vibram FiveFinger Bikila shoes.
The first is not a big deal. Even though the hole is fairly large, it is placed in a place that doesnt affect my running - the toe doesn't pop out of it and get scraped.
The second, on the other hand, hurt a lot. You can see remnants of blood around the edge of the hole.. 2 days later my toe still hurts from the scrape it had.