Single-crafting multiple items in the Workbench by rapidly LMB clicking ignores what feels like every second click (that might just be me not being able to click faster).
Clicking a bit slower does not ignore clicks.

Edit: This also affects the Engineer's Crafting Table

I have a suspicion that this just is how general pickup clicks work in minecraft (try rapid picking up and placing back down items in the same slot in any inventory), and minecraft's crafting pickup clicks change that behavior somwhere
I'm looking into making a fix for this, but in case I don't get on with it
noting this here so it saves you or me a couple of minutes