On today's daf, the Gemara has an iba'ei whether Rav Shimon ben Elazar (RSBE) is lechumra or lekula. The Gemara brings a proof that it's lechumra from a braisa, "mipnei harama'im". Rashi says there that it's bitmiya. According to the way Rashi learned the iba'ei, if RSBE is lechumra as the braisa proves, then RSBE's statement is benichusa. Why does Rashi say it's bitmiya?
The comment of Rashi to which I think you are refering (Rashi DH RSBE) is actually explaining an earlier line in the Gemara, in the words of Rav Yehudah Amar Zeiri, directly after the word "Gomlin" of the previous Rashi.