I'll also be sending this to Project Red Bug Tracker 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.

Can confirm, bug is in the Mekanism itself (compiled last version for 1.7.10, same forge version), used Formulaic Assembler to confirm it's not Project Red bug, same result, if you use bin and 3 blocks on the Formulaic Assembler, it puts 3 in the Bin and this leaves 2 blocks inside the machine on the grid, so you can repeat and get 3 more, each time one block less on the bench (works with any amount of blocks). Also, using Project Bench or Formulaic Assembler to pull out the blocks out destroys the Bin and you'll get maximum of 64 blocks. If you're using Machinist's workbench from Thermal Expansion/Thermal Foundation also destroys the bin. If you're using it to automate puting the blocks into the bin, you can only put two, trying to put third one destoys the block. But maybe they are not really related since if you're using it just to put one block, you can put as much as you want by one, but if you have for example 4 and try to use the Schematic you've created, it'll revert it to the same amount of blocks in the Bin used in the Schematic.

@AsukaLangleyfag Does the Machinist's Workbench from Thermal Expansion also duplicates items?

Oddly, no. You can only put one block at the time. But it's still destroys the bin and it's not the way it should work.

Should be fixed in 1.11.