Fixed in 1.4.
When targeting two breakable windows with Quietus, one window will break and the other will not when hit by the projectiles. The unbroken window will remain indestructible for the rest of the game.
I first noticed this in The Frozen Court. The breakable stained glass windows at the tops of the stairs are right next to each other. When I swung Quietus at them, one window broke but the other did not, even when hit by other weapons. This denied me access to the item behind it.
I wasn’t sure whether to tack this on to the previous bug report about Quietus, but it seems to be a separate issue. In case it does turn out to be related, the window glitch happened when firing Quietus without any blue or green mana, i.e. the other glitch had already occurred.