If the money lost due to error is significant then send a legal notice to the CEO of the company through your lawyer. Tell him that you plan to file a case for cheating under section 420 among others. Chances are that they will send you a cheque for differential amount soon without further trouble.

If the amount is small then send a written complaint to commissioner of police of your town by registered post A.D. In some big cities like Delhi there is a special wing of police known as "Economic Offense Wing" or EOW. Search in google to see if any such police department exists in your city. If yes, then send the letter to EOW. Send a copy of this police complaint to the company. This is a sure method to bring such careless companies in-line without spending too much money.