1)
Why does the Torah mention "them" before "their father"?
1.
Oznayim la'Torah: They knew that they sinned through money (the sale of Yosef), so they were punished through money. Their father did not know this.
2)
Why does it say that they emptied their sacks?
1.
Ha'amek Davar: They inverted the sacks, and all the grain in the Amtachos fell out, and they also found their money. They did not know whether the money was [only] in the sack or [even in] the Amtachas; in any case it was clear that it was in the sack. However, they were afraid that just like one of them (Levi), it was in his Amtachas (the ones who give grain put it there intentionally), also all of them. 1
