Probably because the chisel returns itself to inventory when using chisel recipes. Not sure how to fix it, only workaround is to repair in tool stations.

Can't be fixed because vanilla MC

Thought so. At least, could you block chisels from being repaired that way?

I suppose I could. I just don't see it as a big issue because.. it's only a chisel. ;o

If I understand the problem correctly, you can actually fix this easily using Forge events. Use PlayerEvent.ItemCraftedEvent and check for the chisel as the output, and if it is, decrease the stacksize of the input chisel or set it to null.

Example: https://github.com/squeek502/VeganOption/blob/master/java/squeek/veganoption/content/modifiers/CraftingModifier.java#L55-L93

Oh, good idea. Only solution I found was the crafting handler, but there I can't do that because it'd reduce it before it's pulled out.

Works like a charm squeek <3