Gemara

50b (Beraisa): If a needle was found in the wall of the Beis ha'Kosos, and the wall is punctured on both sides, and a drop of blood is found, it was punctured before Shechitah. (It is Tereifah).

(If Reuven bought this animal, if it was already Tereifah, it was a Mekach Ta'os (a mistaken sale. He returns the carcass and gets his money back.) If a scab formed, the puncture was at least three days before the Shechitah;

If no scab formed, ha'Motzi mi'Chavero Alav ha'Re'ayah (one who wants to be paid must bring a proof).

Kesuvos 76a (Rav Yehudah citing Shmuel): Reuven traded his cow for Shimon's donkey. Shimon was Moshech (brought to his premises) the cow to acquire it. Reuven went to take the donkey, and found that it was dead. Shimon must prove that his donkey was alive when he did Meshichah.

76b - Question (Beraisa): If there is no scab, ha'Motzi mi'Chavero Alav ha'Re'ayah.

If the butcher already paid for the animal, he must bring proof to recover his money. According to Shmuel, the seller must bring a proof to keep his money!

Answer: The case is, the butcher did not yet pay.

Question: Why does the Tana assume that this is the case (without specifying? This is left difficult.)

(Rami bar Yechezkeil): Rav Yehudah misquoted Shmuel. Rather, Shmuel puts the burden of proof on the one in whose Reshus the doubt arose.

Question (Beraisa): If there is no scab, ha'Motzi mi'Chavero...

If the butcher did not pay yet, the seller must bring proof. According to Shmuel, the butcher must bring a proof to avoid paying!

Answer: The case is, the butcher paid. The Tana did not need to specify, for normally one does not give his animal before he is paid.

Rishonim

Rambam (Hilchos Mechirah 20:15): If a needle was found in the Beis ha'Kosos and went all the way through, if there is no scab, it is a Safek. The buyer must bring a proof, for the Safek arose in his Reshus. If he does not bring a proof, he must pay the seller.

Rosh (3:34): If there is no scab, it is a Safek whether it was punctured before or after the sale. Ha'Motzi mi'Chavero Alav ha'Re'ayah, i.e. the buyer must bring a proof. This is even if he did not yet pay for it. The problem was found here (in the buyer's Reshus), so we assume that it arose here, like it says in Kesuvos. The buyer is called ha'Motzi, for presumably the seller did not give the item before receiving the money. We do not force one to pay due to Safek.

Rosh (ibid.): R. Efrayim and Ba'al ha'Itur say that this applies only to Treifos due to wounds, which are uncommon. One does not think to stipulate about them. Treifos due to lesions are common and people think about them. Since he did not stipulate, he pardoned them, and it is not a Mekach Ta'os. The Rambam (Bach - this should say 'Ramban') says that even Treifos due to lesions are a Mekach Ta'os. He learns from one who sold an ox and it was found to be a gorer. All agree that it is a Mekach Ta'os if he cannot claim that he sold it for Shechitah, even though the buyer did not stipulate, and most oxen are prone to gore (Bava Kama 15a). Also, if one sold a slave and he was found to be a thief, the sale stands (Bava Basra 92b). The Gemara suggested that it because most are thieves. It rejected this. Rather, all are thieves. This shows that if it were only a majority, it would be a Mekach Ta'os, even though the buyer did not stipulate. All the more so this applies to Treifos, which are a minority. I hold like R. Efrayim. Regarding Ones (something beyond one's control) that prevents fulfilling a stipulation in a Get, all agree that a common Ones is not considered Ones, for he should have stipulated. There is no proof from an ox or slave. There, the seller knows their defects. The buyer relies on this, and that Yisre'elim do not act deceitfully and swindle. Therefore, he did not stipulate. If the seller does not know (e.g. whether an animal is Tereifah), the buyer must stipulate about something common. If he did not, he pardoned it, like all who buy animals. They do not refrain due to a Safek lest it is Tereifah.

Poskim

Shulchan Aruch (CM 232:11): If Reuven bought an animal to slaughter it, and he slaughtered it and it was found to be Tereifah, if we know that it was Tereifah when he bought it, it is a Mekach Ta'os and he must return the money. E.g. if the Beis ha'Kosos was punctured and a scab formed, it is known that three days ago it was punctured.

Nesivos ha'Mishpat (Chidushim 10): The same applies if he bought it for plowing. The hole is a Mum, for the animal was not healthy. This is only if it is Vadai Tereifah. If it is a Safek, it is not Bitul Mekach. The buyer must bring a proof. However, if one bought it to slaughter it, even if it is merely a stringency to consider it Tereifah, it is a Mekach Ta'os, since in any case one cannot eat it, like we say in Sa'if 12.

Nesivos ha'Mishpat (Bi'urim 3): The Tur did not mention that he sold it for Shechitah. This implies that even Stam, it is a Mekach Ta'os, for a Tereifah does not live and it is not healthy. If so, this is even if he bought it for plowing. The Mechaber mentioned Shechitah, for he wrote in the next Sa'if that even Treifos of lesions (in the lungs), which are Tereifah only due to Safek, nullify the sale. The Shach (306:9) explains that the seller cannot say 'prove to me that it is truly Tereifah', for people refrain from a Safek. This is the ultimate blemish! This is only if he bought it for Shechitah. If he bought it for plowing, the seller can say 'prove to me that it is truly Tereifah and will not live.' The Tur rules that a Safek does not disqualify a sale, therefore he did not need to write that he bought it for Shechitah. Here (the hole in the stomach) it is a Mekach Ta'os whether he bought it for Shechitah or for plowing, and a lesion is not a Mekach Ta'os in either case.

Pischei Teshuvah (6): Nowadays the custom is not to consider it a Mekach Ta'os. In such a case, the custom overrides the Halachah, like we say (Sa'if 19) about eggs in which a chick started to form. (Nowadays, people do not consider this a Mekach Ta'os.) The same applies to other things normally sold closed and sealed 'as is', e.g. boxes with glass sheets for windows, or with Esrogim or similar things. Beis Din in every place must investigate what the custom is.

Shulchan Aruch (ibid.): If he bought the animal within the last three days, or he bought it more than three days ago but there is no scab, and it is a Safek whether it was punctured within three days, Reuven must bring a proof. If he does not, he loses, and he must pay if he did not pay yet.

Beis Yosef (DH ha'Mocher): Rashi explains that if there is no scab, it is a Safek whether it was punctured before or after the sale. The butcher (i.e. the buyer) must bring a proof, for he is the Motzi. Presumably the seller did not give the animal before receiving the money. We do not force one to pay due to Safek. Within three days, Reuven must bring a proof. If he does not, he loses, and he must pay if he did not pay yet. Tosfos and the Rosh hold that in every case the buyer must bring a proof, even if he did not pay yet. The problem was found here (in the buyer's Reshus), so we assume that it arose here. The Rambam agrees.

Beis Yosef (DH Kasav): R. Yerucham says that this refers to one who sold his own animal. If a wholesaler buys and sells, he swears that he did not know, and he is exempt. This is based on Bava Metzi'a 42b. This requires investigation whether we can distinguish between here and there.

SMA (23): A scab never forms in less than three days. Sometimes it does not form even after three days. The Tur and Shulchan Aruch say that it is a Safek. They did not say that surely the wound came in the last three days.

Shulchan Aruch (CM 224:1): The one in whose Reshus the Safek arose must bring a proof. If Reuven traded his cow for Shimon's donkey, Shimon was Moshech the cow, and Reuven found the donkey dead, Shimon must prove that it was alive when he did Meshichah. The same applies to all similar cases.

Rema: Some say that since Reuven acquired the donkey (through Shimon's Meshichah), wherever it is, it is in his Reshus, so he must bring a proof.

Shulchan Aruch (2): If a needle was found in the Beis ha'Kosos and went all the way through, if there is no scab, it is a Safek. The buyer must bring a proof, for the Safek arose in his Reshus. If he does not bring a proof, he must pay the seller.

SMA (9): All agree to this law. According to the first opinion in Sa'if 1, it is because the hole was found here (in the buyer's Reshus), so we assume that the hole arose here. The latter opinion holds that since the Safek arose only after the buyer did Meshichah, he must bring a proof.