Lost by decking out, before shrines triggers
There was an occasion where where I had no deck, but I was suppose to win, since the rules say "Once a player's library is empty, that player doesn't lose the game until they try to draw a card and can't."
In my upkeep, I had the 2 black shrines, and another 4. My opponent had only 3 life, it should be enough so he dies in my upkeep, before I draw. But I lost instantly, before any upkeep trigger.
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Raeith#83602 commented
The new shrines (Sanctums) mostly trigger "At the beginning of your precombat main phase" so you'll die from draw step before they trigger. (Exception for [Sanctum of All] which triggers "At the beginning of your upkeep")
The old shrines (Hondens) trigger "At the beginning of your upkeep" which might be why it isn't behaving as you had expected.