I have noticed from time to time that I can't make something if I am about to use the last of a required component.
example say something needs 10 leather pieces and it says I have 10 leather pieces left. It won't let me use them until I have 11 pieces of leather left.
Just a thought. And are you on the PC or console?
I have also noted sometimes if you add an item through a console command, the workbench does not notice.
Sometimes, if you have only the required amount, it glitches out and won't create it. Happens a lot with construction mostly.