If you purchased two tickets, one from Hyderabad to Mumbai on Jet Airways, and a separate ticket on Air India from Mumbai to USA, Air India has no obligation, whatsoever, to accommodate you if your Jet Airways flight is late. Your AI contract is to get you from Mumbai to Newark, not from Hyderabad to Newark. So, if you arrived after check in was closed, they feel it is your responsibility, not theirs. This is one of the risks taken when purchasing separate tickets to save money.
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