No worries. It's very common.
If possible, don't dimple the holes. But if you did miss it and dimple the holes, don't worry. nearly everyone has dimpled these holes accidentally.
You can choose to leave them dimpled. They are opened up later for screws (#6 I believe). If you read on the forums, there is a growing trend for folks to not install so many screws in the fairing that attaches there. They just install the most forward screw and aft screw and omit the rest. So that would mean that you can leave the majority of these holes dimpled and riveted.
Another option which I chose was to flatten out the dimple. Use a flush set of dies on your squeezer. You can get away with doing this once....but don't attempt to dimple these holes again as you will cause cracks.