Based on the information you provided, it seems that the transporter (service provider) has made an incorrect GST invoice. According to the GST rules, the place of supply of services by way of transportation of goods is determined by the location of the recipient, if the recipient is a registered person1. In your case, both the supplier and the recipient are located in Pune, Maharashtra, which means it is an intrastate supply. Therefore, the transporter should have charged CGST + SGST, instead of IGST, on the invoice. Charging IGST on an intrastate supply is not fair and may lead to tax evasion or double taxation2.
You can report this issue to the GST authorities or ask the transporter to rectify the invoice as per the GST law.