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While Praneeth went down to world No. 6 Anthony Sinisuka Ginting of Indonesia, Sameer lost to world No. 8 Jonatan Christie, also from Indonesia.
Sameer Verma retired hurt against Indonesia's Shesar Hiren Rhustavito at the end of the second game.
The Indian shuttler beat Korea's Lee Dong Keun in straight games.
Playing her first tournament since winning the bronze medal at the Tokyo Olympics in August, Sindhu couldn't match her fifth seeded young Korean rival.
Sameer will lock horns with Tommy Sugiarto in the quarterfinals.
Satwiksairaj Rankireddy and Ashwini Ponappa stunned world No. 6 pair of Peng Soon Chan and Liu Ying Goh of Malaysia in a nail-biting mixed doubles quarterfinal.
World No. 31, who had shocked Malaysia's eighth seed Lee Zii Jia in the opening round, needed just 39 minutes to see off Rasmus Gemke 21-12, 21-9.
'I’m not getting much support from the state association because I don’t play for Kerala. If there is nobody to support you, the job becomes easy for the people who are looking to sideline you,' says Prannoy.
London Olympics bronze medallist Saina Nehwal secured a straight game win over Ukraine's Maria Ulitina to storm into the women's singles quarterfinals.
Kidambi Srikanth, Sameer Verma and H S Prannoy faced crushing defeats in their opening rounds, while Saina Nehwal, India's lone contender in women's singles, also failed to clear the first hurdle.