Do you mean Nifong rifled through the rape kit, removing items he found "troublesome" before sending it to the SBI? Pretty outlandish theory, but watching Nifong so far "highly possible," as I sincerely believe there is something pathological about his behavior.
I can't imagine Nifong taking out the semen sample from the rape kid before sending it along for analysis; he hoped it would contain the DNA of the players.
But it's almost unimaginable that the first DNA tests came back negative for semen. If defense attorneys got the first analysis back from Nifong's office instead of from the lab, however, he could have removed the section which talked about semen presence which DIDN'T match the players is the scenario I'm picturing.