4.
General penalty up-to Rs. 25,000/- u/s 20 (xxi) of the IGST Act, 2017 (read with Section 125 of the CGST Act, 2017) can be levied in given situation.
As concerned supply is covered under IGST Act, no penalty under CGST ort SGST Act can be levied.
Moreover, quantum of penalty to be levied is "up-to Rs. 25,000/-" and same is not mandatory. Officer can reduce the amount or drop it al-together.
One can rely on Section 126 (1) of the CGST Act, 2017 read with 'Explanation (a)' thereunder to explain to the officer that no penalty should be levied in given circumstances considering it was minor breach with zero tax-amount involved (this is assuming that concerned goods were exported without payment of any taxes under LUT).
If concerned goods were exported with payment of any taxes and you already got refund there-against, you can try very same explanation to seek no penalty u/s 126 (1). And if officer does not agree, you may seek penalty of some minor amount (say Rs. 500/- or Rs. 1,000/-) as allowed u/s 126 (2).
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.