The Gemarah in Bava Metziah 95b bring an argument of Amoraim between Abaye and Rava who base their respective opinions on the Tanaim Rav Yoshiya and Rav Yonasan. The Gemara tells how they hold of these Tanaims' methods of expounding on Scripture.
However, in Rashi, he has a different text for when the Gemarah says the words:
רבא סבר לה כר' יונתן ומתרץ לקראי כר' יונתן
which implies that Rava holds of Rav Yonasan's way of expounding Scripture. However, Rashi has the following different text:
ורבא מתרץ להו בתר דעתיה דרבי יונתן
which seems to imply something completly different, in that he does not hold of Rav Yonasan's opinion, rather in this argument, he bases his side of the argument on the opinions of Rav Yonasan, and not that he himself holds of this opinion. As it says he 'goes after the opinion of Rav Yonasan'. And so, at face value, it would seems the text Rashi brings is adding a nouvelle addition.
However, later on in the Gemarah, on 96a in the Gemarah's re-quoting of this section of Gemarah, to discuss Rava's angle of the dispute, the Gemarah bring the same words:
רבא סבר לה כרבי יונתן ומתרץ לקראי כרבי יונתן
However, the peculiar part is that Rashi no longer has the words that were mentioned earlier, rather the same text that the Gemarah has maintained until now:
רבא סבר לה כרבי יונתן
So in conclusion, the contradition in the text Rashi has seems quite puzzling, becuase it is unclear wheather Rava is using Rav Yonasan's opinion to win the present argument, or if he holds of his shitta le'halachah.