Makkot 13B

[ישנן] בכלל מלקות ארבעים, דברי רבי ישמעאל.

are included in the category of those liable to receive 40 lashes for violating a Torah prohibition. This is the statement of R' Yishmael.

רבי עקיבא אומר: חייבי כריתות (ישנו) [ישנן] בכלל מלקות ארבעים, שאם עשו תשובה בית דין של מעלה מוחלין להן. חייבי מיתות בית דין אינו בכלל מלקות ארבעים, שאם עשו תשובה אין בית דין של מטה מוחלין להן.

R' Akiva says: Those liable to receive karet are included in the category of those liable to receive 40 lashes, because if they repented, the heavenly court absolves them of the punishment of karet. Therefore, karet does not absolve them of the punishment of lashes. Those liable to be executed with court-imposed death penalties are not included in the category of those liable to receive 40 lashes, as even if they repented, the earthly court does not absolve them of execution; and one is not punished by the court twice for performing the same transgression.

רבי יצחק אומר: חייבי כריתות בכלל היו, ולמה יצאת כרת באחותו ⁠– לדונו בכרת ולא במלקות.

R' Yitzḥak says that like those liable to be executed, those liable to receive karet are not flogged. Those liable to receive karet for incest were included in the generalization: “For anyone who performs any of these abominations, the souls who do so should be excised [venikhretu] from among their people” (Leviticus 18:29). Included in that category is one who has sex with his sister. And why then did the halakha of karet with regard to sex with one’s sister emerge from the generalization and receive specific mention: “And a man who takes his sister…and they should be excised before the eyes of the children of their people” (Leviticus 20:17)? It is in order to sentence one who has sex with his sister with karet, and not with lashes. This is the source for the opinion that those liable to receive karet are not flogged.