The Mishna on 28a states that if one is not a "mumcheh" and is matir a bechor
by mistake, he must pay back the owner from his own funds.
In discussing how much he must pay, the Gemara at the top of 28b quotes a Beraisa that
says that he must pay 1/2 for a large animal and 1/4 for a small animal. Why 1/4? Because of "gezeiras m'gadlei beheima daka".
Rashi gives two interpretations. The second, which is also the Rambam's interpretation
(see Hilchos Bechoros 3:6), is that we fine the owner of a sheep or goat an additional 25%
because they violated the Gezeira prohibiting the raising of sheep and goats in Eretz Yisroel.
The problem we had with the Rambam's interpretation is that it seems to fine the wrong person. It is the Kohen who is the owner of the Bechor but the Kohen is not the one who violated the Gezeirah. It was the original owner, the Yisroel, who violated this Gezeira
and then gave the Bechor to the Kohen. Why is this the Kohen's fault? In the lashon of the Gemara, "Mai Hava Lei L'Mevad". Why should the Kohen lose 1/4 of the damages due him
because of someone else's violation?
Daf Yomi Shiur
Cong. Or Torah
This indeed is a very difficult (or, as they say, "bavuste shvere") Rashi. The Brisker Rav among others asks your question and does not answer. However, with regard to the Rambam, although the Kesef Mishneh says that the Rambam follows the second Pshat in Rashi, many point out that the wording of the Rambam himself implies that he does not follow Rashi. This is because the Rambam also includes the Halachah of half for a Beheimah Gasah in the Gezeirah. This is obvious, as the Rambam adds "she'Lo Yeshahenu." This is a Gezeirah which we do not find in the Gemara, and, as the Steipler Ga'on points out, it must be talking about during the times of the Beis ha'Mikdash, for there can be no Gezeirah she'Lo Yeshahenu nowadays without a Beis ha'Mikdash.
In addition, if Megadlei Beheimah Dakah are penalized just for raising the animals, then why is this Halachah only in a case of Gerama, where it was slaughtered without the permission of a Mumcheh? Even if one was Mazik it directly, b'Yadayim, he should be penalized for raising the animals and he should receive only 1/4th. Moreover, as the Brisker Rav points out, if he actually took it to the Chorshim, then why should he be penalized?
I will get back to you if I have any insight into the issue.