I don't remember all the details but the basic idea was that the Gemara uses "upon her" (עליה) for a Gezeira Shava. (גזירה שווה) The Gemara says: "Just like in forbidden relations, a sister is forbidden, so also by yevamot a sister is forbidden."
The Tosphot Yeshanim asks: "Let's turn the Gezeira Shava in the opposite direction to make her permitted in Yibum? He answers the Gemara is depending on a later page in the Talmud (sugia) in which we know the a positive prohibition pushes off a negative prohibition. So that is what we would think even without the extra words "upon her."(עליה) So why do we need upon her? Only to tell us something different from what we would have thought, -and that is to make her forbidden.
At this point I asked: But what happens after later on the Gemara says a positive commandment does not push off a negative commandment that has karet (being cutting off from ones people) as part of it penalty? After we know this, then without "upon her" we would already know he is forbidden. So what the the "upon her"(עליה) tell us? That she is permitted!