One of the main reasons this happens is because the dough has been handled too much. We have made these many times and sometimes they are super smooth and sometimes they have a few wrinkles in them. But, they are always delicious. Be gentle when you are forming the bagels and you will have a smoother result. You also need to make sure that the water is not boiling too aggressively when you put the bagels in. You want a gentle boil, not a rolling boil, as this will throw the bagels around.