The carbon in this mod and the graphite from Krastorio overlap poorly, and with the mentioned mod you need carbon (unlocked via oil processing, a green science tech which needs circuits to make) to make circuits. Circular crafting.

Krastorio explicitly says it doesn't work well with Bob's.

And for just Krastorio with my mod, there is no issue. Circuits with only those 2 need Wood, Iron, and Copper. Graphite also doesn't exist in Krastorio, something else is adding it.

I'm not sure what you're expecting, you are using an explicitly unsupported mod combination. And even if you weren't, this frankly isn't my problem to fix. I don't remove recipes or mass-replace carbon ingredients or results. If Bob's makes circuits use carbon, it should be adding a way to get it when you need it.