I don't think so, as long as different sectors represented by unique flight numbers are involved. However, routes like MAA-BRU-JFK or MAA-BLR-PNQ are marketed as a single MAA-JFK or MAA-PNQ flight, so in spite of the stop, it is only credited as one flight. I've managed to work around this by taking MAA-BRU one day before BRU-JFK, and MAA-BLR on the previous flight that day. This way, I've got 2 flight credits.