The question came to mind following today's game between Vishy (Viswanathan Anand) and the young Raunak Sadhwani at the Isle of Man 2018 Tournament. Has Vishy been beaten by an Indian player since, say, the mid-90s?
The answer is: Yes
Krishnan Sasikiran vs Viswanathan Anand FIDE World Cup-C (2002), Hyderabad, rd 2, Oct-05 King's Indian Attack: Yugoslav Variation (A07) 1-0
Given this question was asked a while ago, the answer has obviously changed. Pentala Harikrishna won a classical game against Anand in the 37th European Chess Club Cup 2022, held on October 2022. Apart from that, Vidit Santosh Gujrathi won a blitz game in 2019 at the Grand Chess Tour Tata Steel Chess Indian Blitz.