It depends on whether and to what degree indexes are affecting price discovery:
If prices are being set predominantly by active investors who are truly buying and selling based on bottom-up, security-level research, then the percentage of assets that happens to be invested in passive funds is not that important, because price discovery would be working exactly as you and I would hope.
But if prices are being set predominantly by (a) active investors who are chasing indexes because they don't have a choice, (b) active managers who are being forced to sell positions to cope with a high rate of redemptions (from investors who plow that capital back into passive strategies), and (c) traders who grasp this dynamic and shrewdly exploit it for as long as possible; then price discovery might not be working as we would hope. Prices would no longer be reflecting perceived risk; they would be reflecting the (temporary) influence of this once-in-history dynamical process.
Burry makes a compelling case, I think, that the latter is a more accurate description of the current state of financial markets than the former, and that this state of affairs can only persist so long as capital continues to flow from active to passive strategies at such high rates. Globally, assets under management are not infinite, so capital cannot flow indefinitely from active to passive strategies: Sooner or letter, this dynamical process must exhaust itself.