Odd thing, not sure how it happened. Crafted Knight's Bread for the first time, among a series of other crafts, and later noticed it was the only new food item in my inventory not divisible by 3. Did the craft again to check, and could not reproduce (crafted 3 that time) No, I didn't accidentally eat one, since you can't eat while crafting.

Time: Aug 23, 2016, ~11:00 pm PDT.
Frequency: Only once, seemingly
World: Mateus
Character: Hashmael Lightswain
Class/Level: CUL/44
Race: Elezen M
In-Game Time: Let's say somewhere around 3 pm. Definitely daylight
Area: Limsa Lominsa Lower Decks, about 7.5, 15.3

Steps: Crafted Mugwort Carp HQ (received 3)
Finish crafting, eat Mirror Apple (forgot that food bonus)
Crafted Mugwort Carp HQ x3 (receive 9 more, total 12)
Crafted Knight's Bread HQ, only receive 2

I'm not really chuffed at missing the item, no big loss. Just an odd occurrence, maybe the info can help dig up some obscure little glitch. Would've included chat log for the craft, but I don't have any chat tabs with synthesis progress on.