When playing Disney Infinity (2.0 Edition) on an Xbox One in multiplayer (2 player) mode with two controllers, the player one controller appears to no longer control the game (pausing, quitting, etc.).
This issue occurs when the player with the second controller logs into player one's profile. Since the second controller is now logged in as player one, the control of the game has shifted to that controller. When joining a game as the second player, make sure to log into a different account than the first player or play as a guest.