INCORRECT GSTIN

Suppose Mr A have have two businesses one in his Own state say Guwahati with GSTIN No. say 18XXXXXXXXXX1ZY and his other business was in Meghalaya With another GSTIN 17XXXXXXXXXX2Z1 held under his own PAN card.

So he completed one contract work in Meghalaya under this GSTIN No.17XXXXXXXXXX2Z1 so now now the concerned office passed his Bill due to this work done by him say ₹1000. with GST Charge of 2% (=2%1000 = ₹20)
which implies the contractor received ₹980.

My question:( ERRORS INCASE)

What happen when the office file this 2% GST return for Mr A with this GSTIN No.18XXXXXXXXXX1ZY instead of This GSTIN No.17XXXXXXXXXX2Z1 where he had completed the work.