Indigo probably doesn't upload the flight manifest to the BoI system until some point so the immigration officer doesn't see the pax in their system until T-3h. The BoI website used to have the technical information for airlines but that is gone now. I remember running into this problem in DEL some years ago both on (early) arrival and (early) departure. The officers scans my BP to start the processing and then frowned: 'manifest not loaded' Then yelling at a collegaue a few feet away: Is the manifest for flight xx 1234 not loaded yet? I have a pax here!. 5-10 min later after some arm waving and computer typing the data was either uploaded or they found a way to do a manual override to let me thru.