In a syllable with three consonants like ṣṭra, ndra etc. the anudatta collides with the ra-ottu, thus the vedic sign isn't distinct and looks the ra-ottu is extended below, the vedic sign anudatta can be placed little left so that it is visibly distinct.
Look like this issue is fixed, please reopen if you have other thoughts. I used the font in this directory. Attached a screenshot of the current render.
Font
NotoSansKannada-Regular.ttf
Where the font came from, and when
Font Version
Issue
Character data
ಇನ್ದ್ರಂ॒ ಇನ್ದ್ರ॒ ರಾಷ್ಟ್ರೇ॒ಽಸ್ಮಿ