Suppose one wakes up Sunday morning and realizes they never prayed Maariv Motzai Shabbos. As per "Ata Chonantanu after havdala", there is still a requirement to say Ata Chonantanu even if one heard Havdala. When he prays 2 Shemona Esreis at Shacharis, in which one does he say Ata Chonantanu? The first one he is saying is for Shacharis and the second one he is saying as a make up for the missed Maariv Shemona Esrei. Does he say Ata Chonantanu at the first possible time, or is the first possible time the second Shemona Esrei which is the make-up Shemona Esrei? (sources)
According to the Kitzur Shulchan Aruch (21:6), you'd say it in the second prayer, not in the first.
אם שכח ערבית במוצאי שבת מתפלל שחרית שתים ואומר בתפילת התשלומין אתה חוננתנו לפי שמעיקר התקנה צריך להבדיל בתפילה
If one forgot to say Maariv on Motsa'ei Shabbat, he prays two Shemoneh Esreis in Shacharit and says "Atah Chonantanu" in the compensatory prayer [ie. the second one], because the basic requirement is to recite Havdalah during the Shemoneh Esrei.
In the notes to the Artscroll Kitzur Shulchan Aruch (21:6, note 29), they bring the opinion of the Mishnah Berurah, who says that it depends on whether havdalah on wine was made on Saturday night (I have not read this inside):
Mishnah Berurah (108:33) cites opinions that if one misses Maariv on Motza'ei Shabbos, Atah chonantanu is no longer recited at all - neither in the Shacharis Shemoneh Esrei nor in the compensatory Shemoneh Esrei. In a later Siman (294:2), however, Mishnah Berurah follows a middle approach, and rules that if one did not recite Havdalah on wine, then he recites Atah chonantanu in the compensatory Shemoneh Esrei. However, if he already recited the Havdalah prayer over wine, he does not recite Atah chonantanu in either Shemoneh Esrei.