To which Se'ir ha'Chatas is the Pasuk referring?
Rashi #1 (citing Zevachim 101b), Seforno and Rashbam: It is referring to the goat of Musaf of Rosh Chodesh. 1
Rashi #2 in Pesachim, 23b: It was the Sa'ir of Nachshon. 2
Targum Yonasan: Although all three Chata'os goats (of the Musaf of Rosh Chodesh of Nachshon and of the people) 3 were burned, Moshe asked only about the Chatas of the people. 4
See Na'ar Yonasan.
The Gemara in Zevachim, 101b learns from "ve'Hinei Soraf" (singular) that only one of them was burned.
Peirush Yonasan: Some explain Targum like R. Nechemyah in the Sifra - that it was burned due to Aninus; if so, all three were burned; (Hashem permitted eating the Minchah in Aninus, but not other Kodshei Sha'ah. (PF) Rashi (refer to 10:16:151:1) explains why Moshe asked only about Se'ir Rosh Chodesh.) Others explain the Targum 'all three of them', i.e. Aharon and his sons, burned Se'ir Rosh Chodesh.
Why was the Se'ir ha'Chatas burned?
Rashi #1: Because it became Tamei. 1
Rashi #2: Because Aharon and his sons were On'nim.
Rashi (pn Pasuk 19): This opinion holds that if it were Tahor, they could have eaten it at night, for Aninus Laylah is Mutar Min ha'Torah. See also Ramban and R. Chavel's footnotes. Da'as Zekenim - why was it burned? Korbanos Tzibur are offered [even] be'Tum'ah! (I do not understand his difficulty. They are offered be'Tum'ah, but not eaten be'Tum'ah, except for the Korban Pesach! - PF)
What is the significance of the double expression "Darosh Dorash Moshe"?
Rashi (citing the Sifra): Moshe wanted to know on the one hand, why the one was burned and on the other, why the others were eaten. 1
Moshav Zekenim: This is difficult however, since, seeing as Moshe had instructed them to eat them, in which case, he only had one question? See Torah Temimah, note 42 who explains the Sifra to mean that Mah Nafshach, if Aharon thought that the Hora'as Sha'ah permitted eating the Chatas in question ba'Aninus, then he should have eaten them all, and if not, then he should have burned them all. See also Sifsei Chachamim, who cites the text 'why the others were not eaten and who elaborates.
Why did Moshe address Elazar and Isamar, and not Aharon?
Rashi: In deference to Aharon he turned towards his sons and vented his anger. 1
Oznayim la'Torah: Because as opposed to the Kohen Gadol, who is permitted to eat ? and not to eat ? from any Korban that he pleases, the Kohanim Hedyotim are obligated to eat from each and every Korban that there is.
See Sifsei Chachamim.
Why was Moshe angry?
Rashi: Because he saw that the Chatas Rosh Chodesh had been burned ? and he had instructed them to eat th Minchah ? and he erroneously thought ? this included all the Korbanos of that day, even the regular ones. 1
What were the repercussions of Moshe's anger?
Rashi (in Pasuk 20): 'Because he was angry, he erred'. 1
Refer also to 10:20:2:1*.
Why does the Torah insert the (otherwise superflous) words "al Elazar ve?al Isamar B'nei Aharon"?
Sifra: To teach us that Moshe was also angry with Aharon ? Kal va'Chomer from his sons. 1
See ha'Torah ve'ha'Mitzvah. See also Torrah Temimah, note 45.
Why does the Torah insert the word"ha'Nosarim" again?
Sifra: To preclude Pinchas, who is not included since he had not yet been appointed a Kohen.
Why does the Pasuk add the word "Leimor"?
What is the significance of the fact that the middle words of the Torah are "Darosh Dorash" - as the Gemara in Kidushin 30a points out?
Moshav Zekenim: "Darosh" is in the former half, and 'Dorash' in the latter half 1 - to teach us that, even though the generations before you expounded reasons and secrets of Torah, ayou should expound, and receive reward! "Salseleha u'Seromemeka" (Mishlei 4:8).
They are far from the middle! Daf Al ha'Daf (citing R. Y. Alter) - it is the middle pair of doubled words. Chofan Aharon - it is the middle of eighty-nine such pairs of words with the same root, - such as "Remes ha'Romes"; if the roots are different - such as "Lech L'cha", it is not counted, even if they are spelled the same.
QUESTIONS ON RASHI
Rashi writes that the Pasuk refers to the goat of Musaf Rosh Chodesh. Perhaps it is the Chatas of the Mi'lu'im, or of Nachshon?
Rashi (on Pasuk 17, citing the Sifra): It says (Pasuk 17) "Laseis es Avon ha'Eidah" - Se'ir Rosh Chodesh atones for Tum'ah - "Lechaper Aleichem" 1 (Bamidbar 28:22). The others were not for Kaparah. 2
Rashbam: The Chatas of the Mi'lu'im and that of Nachshon, were both eaten.
According to the opinion that it was burned due to Aninus (no one could eat it), it cannot refer to the others, which were Kodshei Sha'ah. It was permitted to eat them in Aninus! (This is unlike one Perush of Targum Yonason - refer to 10:6:1:2*. - PF)
Even though that Pasuk discusses Musaf of Pesach, R. Yehudah (the author of a Stam Sifra) equates the Chata'os of Rosh Chodesh and the Regalim (Shavu'os 2a. - PF)
Sifsei Chachamim: It says about Korban ha'Am (including Chatas ha'Milu'im) "ve'Chaper Ba'adam" (9:7)! That is not true Kaparah, rather, mere cleansing and Hechsher. (Our texts of Sifsei Chachamim say "Ba'adcha". Surely this is a printing mistake; that refers to the Eigel Chatas of Aharon! - PF)