The Vilna Gaon (Gra) has a quite challenging comment on Midrash Seder Olam Rabbah 3:2 that Rashi says the Makkot were twelve:
I haven't found this Rashi anywhere explicitly in him Chumash peirush.
However, the closest I could find to the Gra's statement on Rashi is the one in Shemos 11:9: למען רבות מופתי: מופתי שנים, רבות שלושה מכת בכורות וקריעת ים סוף ולנער את מצרים
Where did the Gra find that Rashi said there were twelve? And does Rashi deal with other sources saying there were more than twelve plagues?