When crafting in the arcane crafting terminal if you use the right click to pull out a full stack (instead of something like shift click) it will consume two items of the product. so if you craft a stack of stone bricks it will only give you 62. It only consumes the items on right clicking to craft a single stack at a time, not on any other method of crafting.

This seems to only happen when a crafting recipe has more than one crafting component. Creating stone buttons does not cause two to be missing. Creating stone bricks does.This happens on both arcane crafting recipes and normal crafting table recipes.
This happens regardless of whether or not the arcane terminal is hooked up to a network. and does not happen in vanilla crafting table or AE2 crafting terminal.
Tested using only AE2 rv2, latest version, the latest thaumcraft, and the latest thaumic energistics.