The settlement's fatal limitation was its guest list. It recognised two religions: the Catholic Church and the adherents of the Augsburg Confession. Everyone else had no standing whatever.
That excluded the Reformed churches, which were spreading rapidly in the empire in the decades after 1555, and it excluded the Anabaptists entirely, who were prosecuted under laws that both recognised confessions were content to leave in force. A Reformed prince who converted his territory had, in strict law, no protection at all, and Catholic jurists said so.
The problem compounded as the confessional map moved. Rulers converted, territories changed hands, and disputes over ecclesiastical lands secularised after the reservation was supposed to prevent it accumulated without a mechanism to settle them. The imperial courts deadlocked along confessional lines. By the second decade of the seventeenth century the estates had formed armed confessional leagues, and the machinery of the peace had stopped working before the Thirty Years War began.
Westphalia in 1648 addressed the omission directly, extending the settlement to the Reformed and fixing a reference year against which contested church property would be judged. The lesson its negotiators drew from ninety years of experience is visible in the drafting: a religious settlement that leaves out a party growing fast enough to matter is a postponement rather than a peace.