Have the same happening to me right now. This is unfortunately the only thing I could find on google so far.
It seems to be related to recipes missing materials. When I add the missing materials to the network (from inventory through wireless access), they disappear entirely (more than the order would have needed) but the crafting monitor still shows the missing materials and the product isn't there either. I only had the dupe bug once, and I'm not sure on the circumstances, but it could have been connected to a recipe missing materials as well.
Edit: Thought about changing to a newer applied energistics version, but haven't tried yet.