I am doing the only waypoint challenge. Sometimes there is a ship in another ship's parking spot, so the transport goes and sits somewhere. That somewhere might onload or offload cargo inadvertently. So, I put sorters to prohibit the wrong item to be transferred - yet there is still wrong items clogging up my machines. I have screenshots and a save file I can offer if you want to see it in action.

It doesn't always happen, but somehow it might be connected to other ships jumping in and out near it.

Adding in allowed item for both input and output seems to help it a bit - but still gets stuck.