Paid speeding ticket before court date and they still issued bench warrant?

My boyfriend got a speeding ticket in Indiana in his semi truck. It was a payable ticket without appearing in court. I paid it for him on oct 29th and the court date was Nov 4th. I got pulled in his regular truck and they told him that he had a warrant for not appearing in court and failure to pay his speeding ticket. We were in ky when we were pulled and they didn't arrest him but now I am trying to figure out what we need to do because I have the official Payment receipt that they gave. I don't understand why they still issued a failure to appear in court warrant when the clerk said everything is paid in full and the ticket reflects that and she said he didn't have to go to court. Does anyone know what we have to do.