What was the brothers' question about the trouble that Hashem brought on them?
Rashi (to Mishlei 19:3, based on Ta'anis 9a): It is man's sins 1 that bring about his suffering, yet when troubles befall him, he is angry with Ha'Kadosh Baruch Hu, and queries the Midas ha'Din for having brought them on him.
Rashbam: They wondered how this was Midah k'Neged Midah, to give them extra money as a punishment for their sins.
Seforno: They were puzzled that Hashem caused this G-d-fearing man to implicate them in order to take them as slaves 2 - Midah ke'Neged Midah, bearing in mind that they sold Yosef, not out of malice, but because they considered him a Rodef. 3
Targum Yonasan: They said that it is not due to their sin.
Malbim: They understood how the previous afflictions were punishment for their sin. Finding the money was the source of a new accusation against them. They did not understand for what sin it comes.
Alei Shor Vol. II, p.607, from Lekach Tov: A buyer who gets a closed bag of grain should open it, to check! The brothers were culpable for not doing so.
As they specifically stated later (See Bereishis 43:18 [Seforno]).
And their decision not to kill him was an act of Chesed on their part (Seforno).
What did the brothers do to bring upon themselves this punishment?
Oznayim la'Torah: They sold Yosef to the Yishme'elim, and benefited from the money. 1
Malbim (to 42:24): Just like they sold Yosef for money, he pained them through returning their money.
Oznayim la'Torah: Having considered Yosef worthy of being 'sold' into slavery, they should have given him to the Yishme'elim free of charge, or sold him and disposed of the money without benefit from it.
Why did he say, "v'Gam Hinei b'Amtachti"?
Ha'amek Davar: If it were in my sack, I would not worry, for those who gave the grain engaged only with the Amtachos. Since it is in my Amtachas, perhaps it is a plot to make accusations against me!
QUESTIONS ON RASHI
Rashi writes: "'And it is also (Gam) in my pack' - along with the grain." Why explain this way?
Gur Aryeh: The word Gam is extra.
Rashi writes: "'What is this, that G-d has done to us' - to subject us to this libel?!" (i.e., we are likely to be accused of theft). Why not explain that they were shocked by the money itself?
Gur Aryeh: Their exclamation sounds like something horrible had occurred; not like they were surprised to have received a windfall.