I know this question is old however, this might help someone else.
As indiannetizen has rightly pointed -and to elaborate on the same, both invoices are for different purposes and therefore both need to be booked as follows:
1) A GST invoice from Travel Agent (like makeMyTrip.com) will show their service charges as Taxable amount + GST on such taxable services; The Actual flight cost (charged by flight operator, in your case GoIndigo, in the separate GST invoice) is added by MakeMyTrip / Agent as purely reimbursable expense (since flight operator was paid by MakeMyTrip). Hence, GST is not levied by MakeMyTrip on the same (treated as non-taxable charges by MakeMyTrip / booking agent).
Depending on whether the agent reported the bill amount with or without reimpursable portion, (check your GSTR-2A to find out), you should book the expense entry accordingly.
2) As mentioned in point 1 above, for the Actual flight cost (inclusive of GST), you get a separte invoice from the flight operator that you should book as it is.