I'll also be sending this to Mekanism Bug Report about this bug. So basically, as long as you have 2 or more items, if you combine the items and the bin in a Project Bench and shift click the output, the bin will have all of the items you used, but the Project Bench will only use up 1 item. So you can keep doing this bug until you end up with stacks of items. This was done in Minecraft 1.7.10 with Forge 10.13.4.1614. on a server using a custom modpack. You should be able to replicate this glitch by have both Mekanism and Project Red mods installed and using a bin and any 2 or more items in a project bench.

So I start off with a bin and 2 Diamond Blocks

I put the Diamond Blocks and the Bin in the Project Bench which is suppose to put 2 Diamond Blocks in the Bin, this is normal.

I shift clicked the output but 1 Diamond Block is still left in the grid, I put the bin back in the crafting grid and now it says it's going to yield 3 Diamond Blocks.

I placed the bin down, and now I am able to get 3 Diamond Blocks. I started off with 2, then I got 3.

If more information is required, I'll be happy to help.
P.S. - I was using the Sphax PureBDCraft Resource pack with user submitted patches.

Does this only happen when you try and craft that specific item or does it happen when trying to craft anything?

@MrTJP It works on any item as long as it's stack-able and when using the bin and the item inside a Project Bench. I also heard that this bug also happens when using a machine from the Mekanism mod called the Formulaic Assemblicator so this may be mostly a Mekanism issue, I'm not sure.

This is likely caused by the blueprint being too smart and caching the NBT of the created item. This should be resolved in 1.11 and 1.12.