Commentary for Berakhot 57:18

LET US INCLUDE [HAVDALA IN THE BLESSING]: GIVE US UNDERSTANDING. Rav Nachmon said in the name of Shmuel that one can always say haveenainu except at the conclusion of Shabos when one must say havdoloh. The Gemara here asks that he should include the havdoloh in the haveenainu prayer. When the Gemata asks a question it is proof that the Gemara feels that is quite logical to do as it suggests in the question. Otherwise the Gemara would not ask the question. Any question that the Gemara ever asks may be assumed to be a very strong statement that the Gemara considers the point made by the question to be very logical. In this particular case the Gemara does not in fact find an answer to the question. This is even further proof that the Gemara considers the point made by the question to be very logical. Tosfos is troubled by a Gemara in maseches Needoh that doesn’t seem to consider this question worthy of mentioning at all.
And that which the Gemara says in the first perek of needoh (8a) that all year long one prays the entire eighteen b’rochos with the exception of maariv at the conclusion of Yom Kipur, because it is taxing for the congregation because of the fast. And there are those who say that even at the conclusion of Yom Kipur we pray the complete eighteen b’rochos because we must say havdoloh in the b’rochoh of חונן הדעת. And this is bewildering. Why doesn’t the Gemara there ask that we should include havdoloh in the haveenainu prayer as the Gemara is so adamant here, that havdoloh could be included in haveenainu.
Here the Gemara seems to be so sure that it is a very reasonable solution to add havdoloh to haveenainu and there the Gemara doesn’t think of it at all. And we can answer: that there is no comparison. The Gemara here and the Gemara there are looking at the issue from two different vantage points. For there, the Gemara holds that throughout the entire year we always pray eighteen b’rochos, and we should therefore not ask “and we should include havdoloh in haveenainu” in order to change the tradition of the entire year. We usually make every effort to maintain the traditional practice.
But here in our Gemara, where we are saying that throughout the year we do pray haveenainu, the Gemara correctly asks why we should change the custom in order to say אתה חוננתנו, let us include havdoloh in haveenainu. Once again, the thrust of the Gemara’s question is that we should do what is necessary to maintain the tradition of saying haveenainu at the conclusion of Shabos as we do all year.