don't know if you've fixed this or not, but in one of the earlier 1.32 versions I found the following
tested in both the OC and the JEG's training module, not tested in MotB. when using the recipe to craft a regular iron item you only get one instead of the 99 that you would get when crafting with cold iron, etc.
to fix I just made a copy blueprint of the arrow item, deleted the comment of "1" from the item properties, named it as close to your naming convention as possible (to keep it straight for myself) and updated the crafting 2da to use the arrow blueprint I had made. This corrects the issue with arrows.
from my testing bolts also have the same issue, so I'm thinking that all the ammo/thrown will be the same way.