Unit cost is too high and the system itself is not stable , first time it was used one struck its target the way it was meant to but another was shot down as per Rus own info from Telegram. So obviously 1 was flown in a flight trajectory mode that is not suitable for practical use or has less chance of survival in a contested airspace by either not being able to maneuver a lot due to very high speed or by not avoiding/dodging all the AD zones along its flight path.
So you see the issue, ie why we had made our own guidance & control algo on Brahmos. This is key to Brahmos & Onyx sucess (along with very low altitude fly due to optimised ramjet which a scramjet powered missile will not be able to) that it uses DRDO made guidance algo programs in the OBC which decide best course. We have always heard how the Rus were impressed with modifications done by us in many of their products, I think this is another case.
See, that essentially makes S-500 as a BMD asset, rather than AD asset. AD role & BMD role are completely different , which is why our own AD BMD assets are treated as such for deployment. Specialised manpower operate BMD stuff covering the capital & other important place.