Saina and Srikanth's qualification for the Tokyo Games hinged on the Kuala Lumpur event followed by the Singapore Open (June 1-6).
Krishna and Vishnu lost to England's Ben Lane and Sean Vendy 21-19, 14-21, 19-21 in a 56-minute battle.
Former world No. 1 Srikanth cut a sorry figure as he went down 19-21, 17-21 to France's Toma Junior Popov in a men's singles quarterfinal.
Sindhu, the Olympic silver medallist, notched up a 21-18 21-15 win over world No. 13 Pornpawee Chochuwong in her third and final match.
While Srikanth lost 21-19, 9-21, 19-21 to Wang Tzu Wei of Chinese Taipei, Sindhu suffered an 18-21, 13-21 loss to Thailand's Ratchanok Intanon.
Sindhu and Srikanth fought their hearts out before suffering close defeats.
It was Saina's fourth straight loss to world No. 12 Busanan.
Saina's grievances was chiefly about players allegedly not being allowed to interact with their physios and trainers and the reduced practice and gym timings allowed.
Srikanth lost to second seed Chou Tien Chen of Chinese Taipei 22-20, 13-21, 16-21.
Srikanth, seeded fifth, defeated Ho-Shue 21-15, 21-14 in just 33 minutes to make it to the last eight of the Super 750 tournament.