I do have modded chests. There is a Merging Chest for the input items, Pyanodon's Automated Factory is controlled by the CC, and I also use Yuoki's inserters. I did a couple of tests just now, and even if I unmerge the chests, and use vanilla inserters, I get the error.
I'm trying to do a circuit network, that turns the assembler off, after a set number of items are created. I simply put the item to make into a chest, that is wired to the CC with Set recipe. After all the items are done, an inserter takes the one original item out from the wired chest (or I can take it by hand before that). The assembler stops, the raw materials are put in the CC's own chest, and then there's the crash. If I set the CC to discard items, there is no problem.
I have a save, that allows me to reproduce the problem. Can/should I send it to you somehow?
I made a very similar but somewhat simpler arrangement a couple of months ago, in 0.16. It did work then without any problems - including the merging chests and Py's assembler.