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.
Here is a link to a video - you can see my inventory before hand and see that I should create a new stack of pet supplies, but it doesn't when I click one in the second bag. It does work when I click one in the first bag, however.
https://drive.google.com/open?id=0B9sjxPCyyy_keXR6TVpDWlQxZWM
The reason it is gone is because there is no valid space to place the item. In theory it should go to the item scavanger or something . You had no open space in you general collection bags and your other stacks were full as well as the bag itself so the item had no where to go.
First bag is the default, yes, unless you have an auto-collect bag with open slots that has a filter that meets the item's criteria, in which case it will go to that bag instead. [At least, that's how I've observed it in action.]
I have also had pet items go missing upon being opened. My bags are set up with a mix of non-filtered & filtered bags: the first 2 are open (no restrictions so available for anything), other various bags set up for non-gear items, mythic/epic only, gear only, etc. There are a couple of bags near the end of the list that are open with no restrictions just like the first bag.
When I opened the pet item boxes that lost their contents, the "non-gear" filtered bag, where the pet reroll/food item would normally appear, was full. The items did not appear in any of the wide open/non-restricted bags, they simply disappeared.
This occurred both a couple of months ago* and then again a couple of days ago (there was no playtime between). Now that I know it's an actual bug, I will try to get better/more exact information. I don't record my play as my computer is being a jerk and insists it cannot run fraps at the same time as DD2.
*Please note that my memories of this occurrence are fuzzy; although it seems to have happened the same way that time, it's possible that I'm miss-remembering. The more recent occurrence did happen this way, however.
I have not been able to get this to happen, if you can get a video of this that would be very helpful. Thanks!