When the game does auto consume food or drink it uses ALL the food and drink in one shot. Seems like the reuse timer isn't getting reset. I have lost 76 of good food and drink. It will show the message that you eat/drink the item over and over until all your food/drink is gone. I have tried a bunch of times and every time it will use ALL your food and drink instead of just one item. This started happening with the last patch.
Just happened to me too when starting the Plane of Innovation part of the adventure signature quest. I susupect it may be because of the 'Fount of Power' buff. Because it returns to normal consumption when zoning out. Guess I'll just have to turn off food/drink auto consume when doing missions.