I have a system to autocraft things with the project red autocrafters. I request items directly to the crafters but sometimes I believe it is when the output overflows the items get stuck marked as red in the pipes and they wonder for eternity.

Playing tekkit 2 I have a network of matter condensers making some items but when stuff like copper cables or batteries overflow (I pull the items from crafters into a big alchemical chest) the ingredients for the recipe start overflowing. I think that is bcs a bit of items is missing but the whole stack doesn't fit

I now have a system filled with more than a hundred red items just wandering around and I don't know if there is a way to clear it or to prevent more from getting in

minecraft 1.12.2
tekkit 2 v1.0.5

If it's still relevant, I think what you need is a overflow responder chip.