basically the fecal test is looking for eggs.
the worm eggs may not be shed in the feces at all times so it is possible to get a "false" negative(meaning at the time of the sample there just weren't any eggs to be detected)
what also may happen is the treatment will wipe out the mature worms in the GI tract so there is no egg laying but later the immature worms or eggs will mature and lay eggs and start to multiply again, or adult worms that were alive elsewhere in the body have migrated back to the GItract and began laying eggs.
common stuff. no worries. this is why regular fecals are recommended.