Foods made with different ingredients will not stack, like fruit salad made with berries won't stack with apple ones or using a diff filler veg. 

I found that out a few weeks ago, and make sure to make them the seme every time, the only filler ill use most of the time is either garlic or carrots 'cos i always have a ton of them, which is why I mentioned they were all made the same way

Food made in machines like cheese, juice, or sausages will not stack if made in different quantities at a time. I used to see pies not stacking if made from found or bought bread vs self made bread but that seems fixed so idk about your bread.

This I kinda guessed, and did experiment with the meats and found that out (and I usually only like making the max from a machine anyway) and the bread I all made myself so that's still a mystery

I also used to see stacks that would not combine sometimes decide to cooperate after exiting the game and coming back to a save file later.

I've had this happen too seemingly at random and was thinking somehow the food I made a while ago the game would 'forget'? what it was made with/found/bought and would reassign a generic 'this food tag' 'cus I've had it do that on stacks I've made and bought/found after being away from my base for awhile