This happened once before, and I thought I was just going crazy, then it happened again, so now a report!
I'm not sure if this is specific to the Myon cooking station, or all of them, but I've had it happen at least twice now, where I make a collection of items, expecting a certain amount, only to be shorted by one set.
I check the logs, and it shows that I successfully started all of them, but the "you have completed the production" is short one for some odd reason. It just vanishes.
I don't remember what I was making the last time I noticed, Healing Draughts/Potions perhaps? Using the code value. I recall the same issue.
This most recent incident happened while making Huge Bait. I had enough ingredients for 7 creations, for a total of 35 huge bait. The logs showed 7 started productions but it only showed 6 completed. No unfinished products in the pot. I ended with 30 huge bait instead of 35.
If logs are needed, it occurred around the time this was posted.