Concern of Prohibition After seeing a Stain

My wife is taking medication that disrupts the hormonal system. As a result, her period came 50 days after the previous one, and 20 days after stopping the medication.On day 50, she saw a stain in the bath, which was permitted by a rabbi.A few hours later, we had Intimate relations, and a few hours after that, a small bloodstain was found on the towel used during the act.A few more hours later, it became clear that she had gotten her period. Does this mean that the period had already begun at the time we were having intimacy? And if so, is atonement (kaparah) required for this?Please note: I am charedi, and not looking for answers intended for those newly observant.

Shalom 

There is no clear indication that the period began at the time of intimacy — unless the towel was used only by the husband, or the wife used it immediately after.

But if the wife used the towel even with a short time after — even a few seconds — we can attribute the stain on the towel to bleeding that occurred after the act.

In general, the directive of our teacher, HaRav Amrom Fried, in a case where a non-prohibitive stain appears at a time when a period might begin, is to wait 24 hours (or sometimes 12 hours, depending on the case) before engaging in intimacy, to avoid a possible prohibition.

But in your case, based on the details above, there is no reason to be concerned that a prohibition was transgressed.

See Niddah Page 14 and Shulchan Aruch Yoreh De'ah, Siman 185