In Maariv after Shabbos we insert אַתָּה חונַנְתָּנוּ into the Amidah. In some siddurim the word בהם is introduced making it read אַתָּה חונַנְתָּנוּ לְמַדַּע תּורָתֶךָ. וַתְּלַמְּדֵנוּ לַעֲשות בהם חֻקֵּי רְצונֶךָ What is בהם referring to? It seems like in some version there must have been the word like שבתות which has got left out.
Bach (Orach Chaim 294) says that it refers back to מדע תורתך: through our knowledge of Hashem's Torah (besides general knowledge, אתה חונן לאדם דעת, which is equally true of Jews and non-Jews), we are enabled to perform the mitzvos of Hashem's will.
On the other hand, Seder Avodas Yisrael (R. Seligman Baer) states that it is simply a copyist's or printer's error. (In some versions of ותודיענו - the replacement for אתה חוננתנו used when Yom Tov falls on Motzaei Shabbos - the same phrase is used, and there בהם fits better with its antecedent, את משפטי צדקך. So it is possible that the copyists incorrectly applied it in both places.)
R' Hirsch says it refers back to da'as and bina of the first line of the beracha - ata chonen l'adam da'as etc.