nah, a limitation of what's available in the tools. the selection box that pops up can't track exactly the multiple selections you choose when you put ingredients in. there is a C++ implementation in the engine that we can't access (it's game source code) that does something weird with the array of selected items, it gives you the accurate list of uniquely entered items, but no matter what i tried it couldn't accurately report the exact number of each ingredient you select. so i had to work around it by trimming the selected ingredients into just the unique ingredient types put in, and use those to compare against recipes.

tldr;
henry isn't a 1 man super soup kitchen, you have to cook items one at a time

You should ask the game's dev to fix that, it is really disappointing :(

Nah, I guess the engine has a reason for letting you access the contents of an array without pulling out quantities and that's fine, it's not a game breaking bug or anything balance heavy, it's just tedious but then again, more time spent cooking and enjoying the game is fine, I'm fine with it!