Just a quick update on that issue, and additional information.
In the mods settings, I had it set to paste one stack. Recently, I changed it to 5 then 10 for reasons. And guess what? I tried to reproduce it on purpose with these settings but it hasn't happened a single time since.
On the other hand, there is another issue that appeared. It happens sometimes, but when it does, it will do so every single time. I'll describe what happened.
I was using Angel's Big Requester Chest, which is a 2×2, 60 slots chest. So I pasted a recipe from an assembler (two different items, 200 stack size each) with the stack-per-paste setting on 10, so one paste would equal 2000 for each. I pasted it three times, which should have been 6000 and 6000. Problem: at the third paste, the first ingredient was set to 6000, while the second remained at 4000. Any ulterior paste would do nothing. If I cleared the requests (either normally or through the mods copy-paste on the same chest) and tried again, the issue would arise again.
As I said, it happens unreliably so I can't reproduce it nor do I know the cause. Also, I didn't think about trying to remove the chest and try again, but I'll do so and update you on the result if it happens again.
Anyway, that's not an issue at all since it happens so rarely but I just wanted you to know that it happens.