The Mishnah taught: R. Meir says that rape or seduction (of a virgin Na'arah and Motzi Shem Ra require three judges. And the Chachamim say that Motzi Shem Ra requires 23 judges as it can be a capital case.)

R. Mana: They disagree over a betrothed Na'arah...

R. Meir: Three judges are needed to take away her right to her Kesuvah money and 23 are needed to give her the death penalty (of stoning).

Chachamim: The same way she is punished with stoning is the way that she loses her Kesuvah money, but as for Motzi Shem Ra, all agree that there must be 23, even for the husband to receive lashes and pay 100 selah if he is found guilty.

Question (R. Yosi bei R. Bun to R. Mana): But in the Mishnah the dispute seems to be different? (The Mishnah seems only to be discussing his trial and you say that it is discussing her trial?)

Rather, they disagree over (ruling against the husband in) Motzi Shem Ra - R. Meir says that the husband can receive lashes and be obligated to pay the 100 selah with three judges and the witnesses can be put to death by stoning (if they are false) with 23 judges.

Rabbanan: In the same way that the witnesses can be put to death, meaning with 23 judges, the husband receives lashes and pays the 100 selah; but as for the betrothed Na'arah, all agree that in the same way that she receives lashes (with 23 judges), so too she loses her kesuvah money (only with 23 judges).

It appears that R. Mana follows R. Zeira and R. Yosi bei R. Bun follows R. Abahu (in Yerushalmi Maseches Kesuvos Perek 4 Halachah 4 26b-27a. There, we find a parallel dispute between R. Abahu and R. Zeira in the case of Motzi Shem Ra, as to whether the two aspects of payment and stoning can be viewed separately in terms of the testimony of the witnesses.)

Question (R. Abahu): According to R. Meir, when a (habitually goring) ox must be stoned (for killing a person), is the payment given by a ruling of 3 judges (who ruled that he had become categorized as habitually goring) and the stoning given by the ruling of 23 judges?

(R. Yosi bei R. Bun to R. Abahu): The law of an ox that must be stoned is fully a monetary case; however, the Torah decreed that the ox must be stoned.