What was the purpose of the brothers having the money in their bags? It did not get them back to Egypt, they went back for food. So what was the point of this whole ordeal? Further, when they explain the situation, it says they speak to the one 'in charge' of Yosef HaTzadikk's house - who was this, and how did he know they received their money originally. (Bonus: Was the money actually received, or were they just saying that to make them calm?)
Yosef commanded Menashe to put the money in the bags as shown in Miketz 42:25 in order to set the brothers up for the next time that they came. Yaakov suspected that something was wrong so he sent the original money back with the brothers as in Miketz 43:12 besides the new money. When they returned to Egypt, Menashe in Miketz 43:23 pretended to have received the original money in order to set up the next step.
Indeed they denied the second charge in Miketz 44:8 since they had tried to return all the money.
All of this was part of Yosef's plan to test that the brothers had truly repented of what they had done to him and to see that they would protect Binyamin.