I like this idea but it seems hard to differentiate between "You did what you thought was right but you need to be more careful about what you believe" and "you got the bad ending because you missed this little thing", which is something many games have done before.

An example is Iji where the game plays out significantly differently if you make a moral decision not to kill, but if you take the default path it doesn't let you know you could've chosen to be peaceful the whole time. It involves an active decision rather than a secret thing you can miss, but it also doesn't frame it as a "MORAL CHOICE TIME GO"