I've run into a problem with crafting that I believe to be a bug. I had the diagram to make grapeshot bombs. Then I got the diagram to make the enhanced grapeshot bombs. However I can't make any of the enhanced ones, because I didn't have any grapeshot bombs left when I got to diagram for the enhanced version. Now in the crafting menu there is no option to craft the regular grapeshot bombs so that I can upgrade them to enhanced. Is this a bug or am I missing something?

All your bombs refill when you meditate (as long as you have any 1 of a variety of alcohol).

There is a bug with some enhanced recipes, in which the enhanced recipe disappears before you craft the enhanced version. If you ran into that bug, you can try discarding your bombs, then you should be able to make the base and enhanced versions at the same time (as long as you have the components).