The Extruder for example will reserve a bunch of iron and then deny it to everything else on the logistics network. This happens regardless of having anything queued or not. If I take a completed large pipe out of it and put it in the storage container I have connected to the same network it'll take it back and put it in the "done" section. Denying any other producer that may need that item it. Same with wires.

I've rebuilt the entire thing, restarted. Nothing seems to help, everything is just a mess now and I'm forced to move everything by hand if I don't want it to actively sabotage my efforts.