The Dix Hills owner of a used car business that is under state investigation was arraigned Friday in connection with the theft of money from a customer, authorities said.

Neil Sims, 56, accepted extra money from a buyer to pay off the loan on his 2013 Honda Civic, which was being traded in for a 2010 BMW, Nassau police said. He owns 1-800 Preowned, located at 400 W Merrick Rd., Valley Stream, police said.

That deal was made on March 26 of last year, but the victim later discovered the balance was never paid, even after Sims sold the Honda, police said.

Sims, of Hunting Hollow Court, was charged with third-degree grand larceny and first-degree falsifying business records, police said. He was released on his own recognizance.

His attorney, Joseph Carbone of Farmingdale, questioned why his client had to be arrested because the problem was a “paperwork mistake” and the lien on the Honda, $29,306.25, has been repaid.

“There was no intention to steal any money or anything like that,” Carbone said Friday night.

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Earlier this month, the state Department of Motor Vehicles said it was investigating the Valley Stream dealership, now shuttered. The agency said it failed to give proper titles for vehicles sold to at least 48 customers and that additional cases were being investigated. In one case, according to the state, the dealer used the same vehicle to scam two customers.

The agency also cited what appeared to be the Honda trade-in case, saying the new buyer of the Honda did not know a lien remained on the vehicle.

Carbone said all the customers have received their proper titles.

He said Sims was just part owner of the business and was “taking the fall” because he was also the manager.

“They didn’t really need to come and arrest him on this,” the attorney said. “We’ve been dealing with the detectives the whole time. He’s been dealing with the DMV ... There was no reason to arrest him. This was a business problem that’s been resolved.”