Bolas's Citadel + Ninjutsu
While Bolas's Citadel was in play I tried to use ninjutsu of Fallen Shinobi not realizing it had to be from my hand. After I had cast the Fallen Shinobi which came into play not attacking my library disappeared and I was unable to look at it until I played and activated a fetch land to shuffle my library and my library reappeared. This happened once later in the game after the 3rd part of my Elspeth Conquers Death resolved, the library disappeared and didn't come back until the next turn.

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Sandell#81603 commented
Hi, I had similar issue today in the Vintage Cube: Activated Ninjutsu from top of Library with Bolas's Citadel. Fallen Shinobi was cast, and then turn was passed to opponent.
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pizzaofdeath#86230 commented
While Bolas's Citadel was in play I tried to use ninjutsu of Fallen Shinobi not realizing it had to be from my hand. After I had cast the Fallen Shinobi which came into play not attacking my library disappeared and I was unable to look at it until I played and activated a fetch land to shuffle my library and my library reappeared. This happened once later in the game after the 3rd part of my Elspeth Conquers Death resolved, the library disappeared and didn't come back until the next turn.