I'm not at the point where I have Advanced Circuits auto-assembling to stock up, so I went to make some semi-manually.
That is, I deposited the materials into a chest, from which 4 fast inserters pull the materials into 4 blue assemblers, all of which are set to build the Advanced Circuits and then deposit them into two output chests (two assemblers per chest), also via fast inserters (all of which benefit from a +1 stack bonus from my current level of Stack Inserter research). Nothing else draws from these chests and they're not part of the logistics network so I know I didn't just lose track of my inventory.
I put in the exact number of materials necessary to make 100 Advanced Circuits. When the task completed (and I cleard the assemblers to make sure there weren't any incomplete sets of parts in their buffers), I received.... 87 Advanced Circuits. There are no remaining components in the input chest, or in the output chests, or in the assemblers.
Earlier I'd also experienced this with other things I'd crafted in this semi-automated setup, but it was more like a 3% loss, not a 13% loss. It seems to be getting worse as I build my base further. I know this is pushing my computer pretty hard at this point, and I'm thinking that as the game has to process more information with every tick, it's starting to... lose items. (someone also sent me a link to a livestream while I was waiting and I clicked it before thinking about how hard it would tax my computer)
I will also say that I have a number of mods installed, but none of them that I know of affect assembly functions, and none of them have modified the recipe for the Advanced Circuit or any of the components it consumes. They're all untouched. The one mod that affects any of this system is Side Inserters - it allowed me to set up the assemblers and chests in a slightly more compact manner but should have no effect on items or item creation/crafting.
System info: Windows 8.1, Intel Core i7-5557U CPU @ 3.1GHz (dual-core, 4 threads), 16GB memory, 512GB SSD, Intel Iris Graphics 6100
Here's a .zip with my save and all of my mods, in case checking out the actual setup helps: https://we.tl/GSi0vh2TTo
To reproduce (only seems to occur if the computer is heavily taxed): put the plastic, electronic circuits, and copper wire into the chest at the center of the 4 assemblers, wait until they've all been turned into Advanced Circuits. Sometimes they don't stay balanced and the last few Advanced Circuits end up scattered across the assemblers in parts - 4 wire in one assembler, 2 plastic in a second, 2 electronic circuits in a third, for example - but I cleared the assemblers and made sure this wasn't contributing to the issue (which would only make 2 or 3 not be made anyway, not 13).
An easy way to heavily tax the computer, it seems, would be to, say, go to any livestreaming site and watch an active stream while the game is running and doing the above
