Cullen, you must be seeing one of them optical collusions. 
Perhaps, but the OP described them as “round nubby artifacts” and was able to resolve them by running another pass with a clearing bit.
I think @Tod1d may right about the bottom geometry of the clearing tool being the issue.
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OIC. My point was to suggest that those items shouldn’t be seen by the final recipient. Do something to clear it up before releasing the item.
That’s why he asked the question 
The image at the top of the thread is after he ran a cleanup pass. The lower one was to illustrate the problem that he was dealing with when he didn’t run the cleanup. I agree those would have looked better if dealt with.
This is exactly what’s happening! I read your comment, though about it and boy oh boy did I feel silly for always wondering why that happens on occasion. Thanks for the help!
The problem you are seeing is almost certainly that the bit you are using is a so-called ‘fishtail’ bit:
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