The Mishnah (27:9) discusses a case of a garment that is three by three tephachim and was tameh midras. The garment was then torn in two, such that each part was more than three by three etzbaot but less than three by three tephachim. In other words, the parts were still susceptible to tumah, but not tumat midras. According to the first opinion in the Mishnah, the parts are considered maga midras. Recall that a garment that was tameh midras (e.g. due to a zav sitting on it) is considered an av ha'tumah. According to the first opinion, even though the parts are too small to be susceptible to tumat midras, they are nevertheless considered as if they had come into contact with tumat midras. They are maga midras and considered a rishon le'tumah. R' Yosi however disagrees. He explains that once the garment is less than three by three tephachim, tumat midras disappears. Consequently, for these parts to be considered maga midras they would have had to come into contact with something else that was tameh midras, which R' Yosi reasons never happened.
The Mishnah Achrona explains that the first opinion understands tumat beit setarim ("concealed" tumah) can cause a transfer of tumah. In other words, the interface between these two parts was in contact with the complete garment that was tameh midras. The first opinion considers that significant enough to consider each parts as being maga midras. R' Yosi however disagrees, and maintains that tumat beit setarim cannot cause a transfer of tumah.
While the Bartenura explains that we do not rule like R' Yosi, the Rambam (Hilchot Keilim 23: 9) rules that we do. The difficulty with the Rambam is how he rules regarding the earlier Mishnah. We learnt (27:7) that if a small patch that was exactly three by three tephachim was tameh midras and a thread was then removed, and then more fabric was added to complete the garment, the garment is maga midras. Based on our Mishnah it would seem that R' Yosi would disagree, and rule that the garment should be tahor -- this is the understanding of the Bartenura. The Rambam (ibid 23:7) however rules in this case like the Mishnah. In other words, it appears that in our Mishnah the Rambam rules like R' Yossi, whereas in the earlier Mishnah he rule against him.
The Tosfot Yom Tov suggests that the Rambam does indeed rule like R' Yossi. The earlier Mishnah however is different. Just like if one were to remove a small patch from a large garment, it is difficult to ensure it that the part did not come into contact with the garment, the reason why the earlier Mishnah is considered maga midras is based on that concern. The Mishneh Lemelech finds this explanation difficult.
The Mishnah Achrona also understands that the earlier Mishnah is an exception. He explains that the reason why the garment is considered maga midras is out of concern one might confuse this case with the case where the garment was first completed, prior to the thread from the patch being removed. The Mishnah (29:7) rules that in that case garment is maga midras -- and everyone would agree. Since a slight change in the order of events could result in the garment being a maga midras, the Chachamim simply kept the ruling the same in both cases.
The Maaseh Rokeach however provides a different explanation. He cites the Tosfot (Zevachim 94b) who differentiate between whether a garment is torn in two or a piece of cloth. They explain that if it is a garment that is torn, then it is considered like a broken kli and therefore completely tahor. If however it is a small patch, that is not yet defined as a kli, and its size is reduced, then while it is no longer tameh midras, it can still be considered maga midras. The Maaseh Rokeach suggest that that is how the Rambam understands the two Mishnayot. The earlier Mishnah is a small patch whose size is reduced, where as our Mishnah discusses a garment that is torn in two, and therefore considered broken and therefore tahor.
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