When you add Jelly to an item it essentially duplicates the whole stack.

For example,

I have a stack of Cooked Pork Chops,
I input one full stack plus 5 Jelly,
The output is One full stack of Jellied Pork Chops but the recipe only used one Pork Chop and one Jelly. I am on the latest version.

Got this same glitch. Host of our LAN session managed to fill their entire inventory by shift-clicking a stack.

Hm. I'll take a look. I had something like this with meal crafting, so I should be able to fix this at least moderately quickly.