Steps to reproduce the bug:

• Create a Minecraft instance with Forge, MouseTweaks, JEI, and Quark (and AutoRegLib, a Quark dependency).
• Start a creative-mode world.
• Open a crafting table and fill your inventory with items cheated from JEI.
  • 
• Open a crafting recipe that can be shift-clicked into the crafting table, the [+] button must be above an item in your inventory if the recipe gui was not open.
  • 
• Shift click the [+] button and observe extra items are moved into the crafting grid.
  • 

Quark moves items into the crafting grid with its "Better Craft Shifting" feature, but there is no conflict between just JEI and Quark.
Mouse Tweaks must be present to cause the issue seen here, if it's not there then the shift-click puts the recipe into the crafting table without any extra items.

I do not know why this is happening, so I am hoping to try to figure it out with you and @Vazkii

There's a similar issue with MT wheel interacting through JEI's GUI as if it didn't exist (#2), I haven't looked into that yet but I suspect it's the same issue.

I will take a look and submit a PR soon.

Submitted a PR here: #20