I noticed with 0.1.2.3 on 2.7.3 I have a problem with ic2 reactor parts.
It seems some of them differ in NBT after they have been in a reactor. Can be seen in ME and with Hologlasses, too.
This causes the MM to try to find that specific item, but it is not what my ME system autocrafts.
Even if I place all new autocrafted parts into a reactor and then copy that, it still fails on some of the parts since It expects the different one.
Adding in a setting to ignore NBT for Copy (maybe other modes) too, could fix that.
Or try fixing the IC2 reactor parts.
My guess is that newly crafted parts do not have a heat level set. Placing them in an empty reactor could change them to have their heat set to zero. Thus creating the NBT Heat data.