Remember that blemishes are imperfections that occur on the surface of a diamond, whereas inclusions are found beneath the surface of a diamond. For the most part, blemishes are left intact by the cutter.
The cutter has to make a decision as to either taking the time to remove the blemish or simply leaving it in place. Blemishes generally have no affect on the clarity grade so they are often left behind. In more valuable, larger, high-clarity stones, the cutter may opt to remove the blemish to maximize clarity, value, and salability.