CGST/SGST paid when IGST was payable and vice versa :
Interpretation of provisions of ‘place of supply’ and ‘fixed establishment’ are critical in determining whether IGST is payable or SGST/CGST are payable.
A taxable person who has paid CGST/SGST (in SGST Act) on a transaction considered by him to be an intra-state supply, but which is subsequently held to be an inter-state supply, shall be granted refund of CGST/SGST (in SGST Act). This means that he will have to pay IGST and then claim refund of SGST/CGST paid. There is Parallel provision in IGST Law also.
Really, there should be adjustment between State and Centre, instead of asking taxable person to pay ISGT (or CGST and SGST) and then claim refund of SGST and CGST paid (or IGST paid, as applicable). Even assuming there are some difficulties in adjusting SGST with IGST and vice versa, there should be no difficulty in adjusting CGST and IGST as both are paid to Central Government only.
If the receiver had availed input tax credit, refund will not be admissible.