Why did the brothers express remorse specifically about their failure to take pity on Yosef when he pleaded with them for mercy, and not about the fact that they sold him?
Ramban: Because they realized that not taking pity on the cries of their own flesh and blood was the bigger sin of the two.
Seforno: Despite the fact that they considered him a Rodef (in which case they were justified in what they did to him), their lack of mercy to his cries was an act of cruelty, for which they were now receiving the same cruel treatment at the hand of the ruler of Egypt, Midah k'Neged Midah. 1
Ohr ha'Chayim #1: They had concluded that Yosef was Chayav Misah. It was Chesed to sell him in place of killing him! Even though it pained their father, that cannot be the reason for their current affliction, which will pain Yaakov more! Rather, it is due to their cruelty, i.e. not having mercy when he cried. Malbim - Also, he is our brother; we should have pardoned him due to this. Also, we should have had mercy for his affliction (even without his cries).
Ohr ha'Chayim #2: They thought that the reason for their current affliction is the sale - but Reuven was not party to it! Rather, it must be something that also Reuven did, i.e. when they threw Yosef in the pit, surely he cried due to the fear of the fall, the dank air, snakes and scorpions and [imminent] death from starvation and thirst, which is the worst death.
Ohr ha'Chayim #3: Initially, they thought that the viceroy punishes them via his free choice, even though their actions to Yosef were justified. Now that one of them would be handed over to a Nochri, which was very similar to Yosef, they concluded that it is due to what they did to Yosef, i.e. a lack of mercy to his cries.
Rashbam: Since they cast Yosef into the pit, they had now been cast into prison - Midah k'Neged Midah.
Who is "Ish el Achiv" referring to?
Ha'amek Davar: It refers to Shimon and Levi, who instigated throwing Yosef into the pit - in connection with which the Torah uses exactly the same words 1 (refer to 37:19:1:1). They were most cruel; the other brothers merely consented to them. They decided to remain, and the others will return to Kena'an.
Also Oznayim la'Torah leans to say so.
Why did the Torah not record Yosef's crying out for mercy at the time when it occurred?
Ramban #1: Because it is obvious that that was Yosef's reaction.
Ramban #2: The Torah wants to minimize their sin. 1
Ramban #3: It is the Torah's standard practice to omit some details in one place and to insert them in another. 2
Oznayim la'Torah: So it waited until now, when the brothers themselves mentioned it and did Teshuvah on it.
Ramban (to 42:34): The same applies to when they will tell their father, "Sha'ol Sha'al ha'Ish Lanu u'le'Moladteinu" (43:7) (which must have come as a response to 42:11-13, but which we do not find directly in Yosef's words).
Why did they attribute their affliction to their sin only now?
Refer to 42:21:1:5.
Ohr ha'Chayim: Shimon was chosen to be incarcerated, and he is the one who counseled against Yosef, and said [to Levi "the dreamer is coming" (refer to 37:19:1:1). 1
Malbim #1: Initially, they thought that the viceroy does not truly suspect that they are spies; rather he is a cruel ruler who makes false accusations. Now they saw that he seeks to vindicate them and fears Elokim, just he erred. Why did he err only about them, and not the other multitudes of Kena'ani buyers? It must be due to our sin.
Malbim #2: This is Midah k'Neged Midah. Just like our brother was sold through us, one brother was taken from us.
