In certain cases, opening up a pet box seems to lose the reroll/food/upgrade items.
My first two bags are usually setup for picking up the non-legendary items, including pet boxes. All the rest of my bags are set to only pickup legendary items (and most of them are full). I also have full stacks of most of the upgrade items stored. The first two bags have sorting on, as do most of the others.
If the first bag is full and I double click on a pet box in the first bag, it works as the pet box disappears and the item will appear in its spot.
But if the first bag is full and I double click on a pet box in the second bag, I do not get an item if it would create a new stack. I get the message like "Received Gato Spirit vial", but it is no where to be found.