So... If you take any item (Say dirt or something) and try to replace the result item in the crafting table with it you'll pick up the result but the materials wont disappear, meaning you can make a really complex, powerful item multiple times with a single recipe's materials and a lot of worthless items like dirt. One thing to note is this only works properly with items in which the result is 1. HOWEVER, you can get one extra of the item. A similar thing happens but it does actually erase the materials, and for some reason it only leaves behind one of the result, so you only get one extra. I have attached a link to a video I took (It's pretty laggy but it gets the point across).
Link to the recording

I'm aware of this but currently don't have a solution to the problem. I currently don't know any way to 'save' the previous output item and compare it to the current item to see if someone swapped the items.

I'm going to close the issue just so it's not the first thing someone sees when they come to this page (don't want too many people knowing about it), but you can continue posting here if you need to.