What is the ruling on money acquired from selling physical goods in the army, if there was an increase in prices imposed on soldiers without their initial knowledge, and then the seller separated to conduct independent sales with personal profit, with the knowledge of the unit commander?

What you and your colleagues did by adding extra amounts to the soldiers’ pay is a forbidden act and constitutes consuming wealth unlawfully, based on the Almighty’s saying: "And do not consume your properties among yourselves through falsehood." It is obligatory for you to repent to Allah and return the ill-gotten money to its rightful owners. If you are unable to do so, then donate it with the intention that the reward goes to its owners. If you know the exact amount, then disburse it; otherwise, disburse what you predominantly believe will cover it.