No penalty u/s 74 in given situation should be levied. If SCN u/s 74 is issued, same needs to be defended before original adjudicating authority explaining factual position. No interest u/s 50 (1) should be levied in given situation, in view of Section 19 (2) of the IGST Act, 2017.
Taxes wrongly paid in given situation can be claimed as refund u/s 77 (1) of the CGST Act, 2017. However, one needs to pay correct taxes (i.e. IGST), seek relief from interest u/s 50 (1) as well as penalty u/s 74 and then, claim refund of wrong taxes paid (i.e. CGST & SGST) earlier.
Please also see rule 89 (1A) for time-limit to claim subject refund.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.