Mole Came Back (But Smaller) After Benign Biopsy?

A biopsy will only partially remove a lesion.  There is a chance that the mole can recur.  If the mole returns and over time becomes suspicious, it would be advised to have the mole biopsied again or completely surgically excised.   

Not necessarily. Moles can return if the margins were not large enough. The bigger the mole the more margins lead to a greater success. Depending on how much you take out, your chances are less if more margins of normal appearing skin is included in the mole's removal.

If the biopsy of a mole shows a benign mole, then there is no importance to it recurring. It simply signifies that the mole was superficially removed, likely by a shave biopsy, and likely to try to minimize scarring. Dr. Benjamin Barankin, Toronto Dermatology Centre.

Chances are that your mole was biopsied with a shave technique.  This uses a blade to shave off the top portion of the mole to send to pathology.  This technique can leave behind some "roots" of the mole if it was deep, and these "roots" can cause the mole to regrow over time.  Provided that the pathology was completely normal, this shouldn't be a cause for concern.