Sometimes routed crafting pipes will forget to request items, but will expect to get the result. It seemed to happen after reloading the world, and the only fix was to place the items in manually, allowing the item to craft. Any more crafting requests will work perfectly. I was using routed extension pipes in conjunction with the crafting ones, and I am not sure what happens when used without them.

They work fine. Without more info, i can't really help. Either way, I'm going to assume that you aren't using them properly, since it is very confusing without any documentation.