Poor Thomas turns out not to be the father of Justine's child? Out of his own mouth in the beginning
of Peace talks, while not impossible, it is highly unlikely that he got her pregnant. Thomas says that White Court Vamps are for the most part sterile... Possible he is the exception because of who is mother was, but is it likely? He says they were using birth control.. Failure? Possible, but how likely added to the probable low sperm count for Thomas? Justine was lying about using it? Very likely, but at the same time if Thomas was right about himself, still an outside chance.
Did HWWBs/Nemesis arrange for the outside chance of Thomas getting pregnant happen? Very likely, Justine/HWWBs/Nemesis admitted as much. However not said, whether or not Thomas was the father. It would be much easier for Justine to be unfaithful and get pregnant by a guy with a probable normal sperm count, actually the most logical thing for her to do. Thomas wasn't going to demand a DNA test, he would just accept it and become worried to the point where he'd do anything to save her.
Finally, Harry's gut feeling that something was a bit off about Justine when he told her the news about Thomas in the beginning of Peace Talks.. Could it be that her reaction felt off because there was no connection between her child and Thomas, not just the plan.