1) RAVA'S INTERPRETATION OF REBBI YAKOV'S RULING
QUESTION: The Gemara asks why Rava chooses to explain that Rebbi Yakov's ruling means that one is obligated to pay Chatzi Nezek for damage done by a Shor Mu'ad of a Cheresh, Shoteh, or Katan. Why does he not explain that Rebbi Yakov obligates one to pay Chatzi Nezek for damage done by a Tam? (Although the Gemara (39b) assumes that Rebbi Yakov does not refer to a Tam because that Halachah is obvious, the Gemara now reconsiders this position; see Tosfos to 39b, DH ad'Muki.)
The Gemara answers that Rava wants to teach additional points in his interpretation of the Beraisa. Rashi explains that Rava teaches that not only does Rebbi Yakov agree with Rebbi Yehudah with regard to an Apotropos' obligation to pay for damages caused by a Tam, he also agrees with Rebbi Yehudah on two other points: that "Tzad Tamus bi'Mekomah Omedes," and that one is liable for damages caused by a Tam when he guarded it with a "Shemirah Pechusah."
However, the question remains: how does Rava know that Rebbi Yakov agrees with Rebbi Yehudah on those two additional points if it cannot be inferred from the Beraisa?
ANSWERS:
(a) RASHI (DH Ela Chada) implies that Rava assumes that if Rebbi Yakov agrees with Rebbi Yehudah on the first point, he probably agrees with him on the other points as well, even though it cannot be proven definitely. Perhaps Rashi means that since Rebbi Yakov explains the words of Rebbi Yehudah in the Beraisa (according to Rava), we may assume that Rebbi Yakov is a Talmid of Rebbi Yehudah and accepted Rebbi Yehudah's other rulings as well.
(b) The RASH, cited by the Shitah Mekubetzes, explains that it can be inferred from the Beraisa in which Rebbi Yakov explains Rebbi Yehudah's words that Rebbi Yehudah is discussing a Mu'ad and not a Tam. Although Rebbi Yakov finds it necessary to explain Rebbi Yehudah's words, a Tana never explains what case another Tana refers to; rather, Rebbi Yakov must simply be clarifying how much Rebbi Yehudah requires the person to pay. The Beraisa knows, even without Rebbi Yakov's words, the case which Rebbi Yehudah discusses (whether a case of Tam or Mu'ad).
Accordingly, one may reason as follows. If Rebbi Yehudah would be discussing a Tam, it would not be necessary for Rebbi Yakov to emphasize that Rebbi Yehudah obligates one to pay only Chatzi Nezek (since a Tam always pays only Chatzi Nezek). Rather, Rebbi Yehudah must be discussing a Mu'ad which sometimes pays Nezek Shalem, and that is why Rebbi Yakov finds it necessary to add that in this case he pays only Chatzi Nezek. Hence, it is clear from the Beraisa itself that Rebbi Yakov and Rebbi Yehudah are discussing a Mu'ad which one guarded with a "Shemirah Pechusah" and therefore pays only Chatzi Nezek, and Rebbi Yakov must agree with Rebbi Yehudah on all three points.
(c) The RE'AH in the Shitah Mekubetzes explains that Rava infers this from the fact that Rebbi Yakov repeats in the second Beraisa that the Shor of a Cheresh, Shoteh, or Katan pays Chatzi Nezek, even though he already stated that in another Beraisa (the Beraisa which mentions the view of Rebbi Yehudah). It must be that Rebbi Yakov is not just teaching that an Apotropos pays for damages caused by a Shor Tam, but he is adding another point -- that an Apotropos pays Chatzi Nezek for damages caused by a Shor Mu'ad as well (when he watches it with "Shemirah Pechusah").
(The Re'ah explains further that this in fact is the intention of the Gemara (39b) when it explains that Rebbi Yakov cannot refer to a Shor Tam because "Peshita," it would be obvious. The Gemara means that Rebbi Yakov already taught in another Beraisa the Halachah of a Shor Tam, and therefore here he must be teaching an additional Chidush, as the Gemara concludes here.

40b----------------------------------------40b

2) THE BORROWER'S OBLIGATION TO PAY FOR DAMAGES CAUSED BY THE BORROWED OX
QUESTION: A Beraisa teaches that when a person borrows an ox under the assumption that it is a Tam and it turns out to be a Mu'ad, the borrower (Sho'el) pays half of the damages and the owner pays half of the damages. The Gemara asks that the Sho'el should be exempt entirely; he should be able to claim that had the animal been a Tam as he thought it was (until he was brought to Beis Din) he would have admitted to the damage in court and exempted himself from payment, according to the opinion that Chatzi Nezek is a Kenas. The Gemara adds that even according to the opinion that Chatzi Nezek is not a Kenas, he should be able to exempt himself by claiming that had the animal been a Tam he would have chased it away to the marshes, and then the Nizak would not have been able to collect "mi'Gufo" (and the Sho'el would have been able to use the ox in the marshes).
The Gemara answers that the case in which the Sho'el pays half is when Beis Din seizes the ox before the Sho'el is able to chase it away to the marshes.
How does this answer the first part of the Gemara's question? Even after Beis Din seizes the ox, at any time before witnesses testify about the goring the Sho'el still can admit to the Kenas and become exempt from paying ("Modeh b'Kenas")!
ANSWERS:
(a) The RAMBAN (Sefer ha'Zechus, end of third Perek of Kesuvos), cited by the KETZOS HA'CHOSHEN (1:8), cites the Gemara according to the Girsa of RABEINU CHANANEL that it was the "Ba'al Din" (the Nizak) who seized the ox, and not "Beis Din." He explains that if there are no witnesses who can testify that this animal belongs to the Sho'el and not to the Nizak who is presently holding it, the Nizak is believed in court when he claims that this Shor damaged him, since he has a "Migu." He could have said, "I bought the Shor and therefore it is mine," and he would have been believed since he is presently in possession of the Shor. When he says, "The Shor is mine because it damaged me and I am entitled to collect the payment from its body (mi'Gufo)," he is believed. A Migu supports a claim comparable to the way that testimony of witnesses supports a claim. Therefore, if the Nizak seizes the ox before the Sho'el admits to the damages, it will be as if witnesses came to testify about the damage before the Sho'el admits, and in such a case his admission will not be able to exempt him from paying. (The RE'AH cited by the Shitah Mekubetzes here writes a similar answer.)
(b) The RA'AVAD in Kesuvos disagrees with the Ramban and writes that the admission of the Mazik helps even after the Nizak has proof to his claim through a Migu (see TUR CM 399, in the name of RAMAH and ROSH). According to this view, the Gemara cannot be explained in the way that the Ramban explains it even if the Ra'avad's Girsa is that the "Ba'al Din," the Nizak, seized the ox.
The KETZOS HA'CHOSHEN in the name of his brother explains that according to the Ra'avad's own opinion elsewhere, the Gemara can be understood in a simple manner, according to the Girsa of Rabeinu Chananel. The Ra'avad rules that the Kenas of Chatzi Nezek differs from other penalties. Although the Ba'al Din's seizure of the money usually does not entitle the Ba'al Din to keep the Kenas if his opponent admits to owing it, nevertheless the Nizak's seizure of the Chatzi Nezek does entitle the Nizak to the money even if the Mazik is Modeh. (He explains that Chatzi Nezek of Keren is a greater obligation that a normal Kenas, since it is directly related to the amount of damage that was caused. Hence, when the Nizak seizes the ox in this case, the Hoda'ah of the Sho'el no longer can exempt him from paying.)
(c) According to the Girsa of our texts, that Beis Din seized the ox, it seems that the Gemara relates only to the second part of its question and assumes that Chatzi Nezek is Mamon and not Kenas.
How, though, does the opinion that Chatzi Nezek is a Kenas explain the Beraisa?
Perhaps the Gemara means that if the Sho'el admits only after Beis Din seizes the ox, his admission cannot exempt him from paying since he is like a person who sees witnesses coming and hurries to court to admit his guilt before they come in order to exempt himself (so that he will remain exempt even after the witnesses testify; see 75a). Since Beis Din would not have seized the ox unless they had found ample evidence to show the Sho'el's guilt, it must be that this is why the Sho'el hurried to be Modeh; he knew that Beis Din had evidence of his guilt and he was attempting to exempt himself through his admission! The Gemara, therefore, answers the first part of its question as well, since after the animal is seized the Sho'el's admission no longer helps to exempt him.