The answer is "it depends."Yes I did. Is it legal for the police to be taking the customers money
You have not provided enough facts to tell if the what the police did in taking customers' money was legal.
If a customer walked into a gas station to pay for gas or walked into a convenience store to buy snacks, the police cannot just take that customer's money.
But I suspect that the customers who had money confiscated were at the gas station or convenience store for an illegal purpose, hence the misdemeanor charges. How the confiscated money plays into these charges is a question mark.
Again, try to find an attorney in your area who can offer you a low or no cost opinion.