Hello! The title pretty much says it all. I have listed three examples below with the correct Sanskrit and their Latin transliteration, as well as screenshots of what InDesign incorrectly outputs. (and this is with world-ready composer on and Hindi as the document language, which are the only two solutions I have found suggested online)
Note that I was able to partially correct aaditya आदित्य by incorrectly typing the order of 'd' and 'i', but still cannot fix the conjunct.
May this is an issue of ligatures, either it is switched off or the ligatures are absent in that font. I copied and pasted your text into an Indesign document, applied Arial Unicode MS font, and set the World Ready composer and the result seems to be fine, see the attached screenshot