Er, it's not like people can't be caught during the second round or after completion. This is also from McGonagall's point of view and could be unreliable. The time she caught them probably wasn't the ONLY time they had sex within the window of time that would have produced Tracey. It could just be a convenient conceit for McGonagall to be thinking it was during the time she caught them that the girl was conceived, since she only knows of one encounter during the appropriate timeframe.