I made a quick test yesterday and posted my results related to dying pets and how to reproduce it here.
And while I’m at it: this issue is also related to other item spoils in different inventories as reported here.
But related to the dying pets it may also be possible that the crafting process gets canceled, because the food decayed before it could finish. Didn’t tested that, but it sounds reasonable, because the pet also decays within 24h in the Animal Pen.
Edit: Food does not spoil, if it was used for training pets.
Just tested it in Singleplayer with increased item spoil rates for faster results like I did with my linked reports regarding dying cubs in Animal Pens or spoiling food in Thrall inventories.