London Olympics bronze medallist Saina went down fighting to American Iris Wang, 11-21 17-21.
Indian flavour will be missing in the men's section at the Indonesian Open Super Series 500 after the withdrawals of Srikkanth, Kashyap and Prannoy.
Srikanth, seeded eighth in the BWF Super 500 tournament, won his first round match against Brice Leverdez of France 18-21, 21-10, 21-16 in 49 minutes.
Indian men's doubles pairing of Satwiksairaj Rankireddy and Chirag Shetty also made it to the quarterfinals.
The selection trials are scheduled here from April 15 to 20.
Sen, 20-year-old Indian star, registered a 21-16 21-18 win on Thursday.
H S Prannoy lost to German Open champion Kunlavut Vitidsarn 21-15, 24-22 while former World Championships bronze medallist B Sai Praneeth went down to Tokyo Olympics champion Viktor Axelsen 22-20, 21-11.
In the next round, Saina will take on Malvika Bansod, who defeated Samiya Imad Farooqui 21-18 21-9.
The National Commission for Women sought "prompt and strict action" against the actor for using indecent language on social media.
Kashyap and Srikanth went down fighting in the opening round.