If all else is well, I wouldn't worry about muddy stools.  (Do you
mean colour or consistency?).  In either case, we spend too much time
looking at stools, not enough time looking at the "whole baby".  I
guess it is possible that the gut flora has changed.  I would point
out that changing to formula also changes the gut flora.

As a side issue, just a guess, I will give 3 to 1 that the mother
doesn't really need the amoxycillin.

Jack Newman, MD, FRCPC