Which language version of InDesign are you working with? Also, what OS and what type of keyboard are you using? I only use the North American English version with the standard keyboard, and if I choose (for example) Geeza Pro in InDesign, I get the same rectangles with pink highlight that you are getting. The pink generally means that the font is missing or unactivated, but in this case, I think it's slightly different. The rectangles are placeholders for keystrokes that the font doesn't have assigned glyps for. The Geeza Pro font has glyphs that I can access via the Glyphs pallet (Type>Glyphs), but my keyboard isn't set up to access those glyphs directly, so the keys that I type are mapped to those rectangles. If I knew what I was doing, I could probably switch my keyboard settings and/or use a different keyboard and be able to access those glyps directly, but that's beyond my abilities. Then again, it could be that my version of InDesign wouldn't be up to the task either, but I don't know.
There are some users on this forum who will give you a more complete answer, but until they reply, I thought this little bit of info may help you. Sorry that it isn't more.
Can you tell us the exact name of the font? I searched Google for "bapuscript" but can't find any font with that name.
Also, we can't help you much without answers to Michael's question - what operating system and keyboard are you using? Your mention of "Phonetic notation" makes me think that you're using an English keyboard. Some fonts for the languages of the subcontinent are just Telugu or Oriya or etc. glyphs written over the English glyphs - so you whack the Y key and get a telugu ya (య). But that's the 20th-century way of doing things; new fonts actually require you to use the correct input method, instead of just using an English input method. But unless we know what kind of font you're using, we can't guess.