Not entirely sure if you're still developing on 1.7 but it might also be apparent in higher versions,l. To quote one of my players, "Reporting an exploit: Craftingcraft tables let you dupe crafts. Just put a recipe into the table and close out of it. It will return the items to your inventory, but you can still craft the item"

So a bit more information on this, and replication steps. (V1.0.13)
This occurs only in the in-world crafting tables, not the handheld ones.
It can be seen by placing any recipe in the table, then closing the table. At that point the input items are returned to your inventory, but ghost copies still remain in the table.
Ghost Copies (input items) cannot be removed from the grid, as they do not exist.
These ghost copies can still be used in crafting, and a fully working output item is produced.

It's no longer happening in recent versions and I don't think I'll go back to fixing this in 1.7.10 (which is three versions behind at this point), sorry