* The Rabbeinu Chananeil (36a) explains that the Gemara was not explaining the Mishna at all but rather adding another potential disqualification. According to his view, the pitom is on the top of the etrog and “buchanto” is on bottom. He adds that the oketz is the outer part of the stem on bottom, and if that is removed, the etrog remains valid. The Rif (17b) and Rambam (8:7) agree. The Rosh (3:16) writes that the minhag was to follow Rabbeinu Chananeil. Shulchan Aruch (648:7-8) concurs. Mishna Brurah (648:31) writes that if the bud on top of the pitom falls off, one should avoid using the etrog unless it is the nicest one available.
* The Rosh adds that if the etrog grew without a pitom in the first place, it is valid. Rama (648:7) codifies this. Mishna Brurah (648:32) explains that the reason an etrog without a pitom is invalid is either because its lacking or is not “haddar.” Accordingly, if an etrog grew that way initially, it is valid. </ref>
# Some poskim invalidate an etrog that has black dots found on its chotam, while others deem it valid. <ref>The Mishna (34b) explains that an etrog upon which there is a protruding growth (“chazazit”) that covers the majority of the etrog is invalid. The Gemara (35b) adds that if the growth is found in two or three separate places, it invalidates the etrog, since it appears “spotted.” Additionally, the Gemara states, if the growth is found on the chotam, it invalidates the etrog regardless of its size. The Rosh (3:20) writes that a discoloration of white or black has the same status as a growth. Therefore, the Tur and Shulchan Aruch (648:12) write that a discoloration of any size on the chotam would invalidate the etrog.
* What is the chotam? Rashi (35b s.v. Ubechotmo) explains that the line at which the etrog begins to slope inwards is the chotam. See Halachos of the Four Minim (p. 10) for a diagram. The Rosh explains that the Rif holds that the chotam is the entire slope up to its pitom. The Beit Yosef (648:12) writes that the minhag was to be strict for both Rashi and the Rif. The Beiur Halacha (648 s.v. Mimakom) explains that the Rif, and by implication Shulchan Aruch, agree that the pitom itself is included in the chotam.