Way after blowing up The Institute, at the climix of the "In Sheep's Clothing" quest, Kellogg's House Key reappeared on Geneva's desk right before breaking into McDonough's Office before confronting him.

What Happened:

- Kellogg's House Key appeared on Geneva's desk in the wrong quest.

What Should Have Happened:

- Kellogg's House Key should not appear on Geneva's desk in this quest regardless if the player character has convinced Geneva to slide over the keys during that respective main storyline quest.