I have an Extra Utilities pipe going to the back of a 2x2 Storage Drawer. When I put saddles into the system only 1 saddle will be put into a slot, any additional saddle will bypass this drawer. I can still manually put another saddle in the slot. This drawer has been upgraded with a level 6 upgrade (Emerald) if that makes any difference.

I am not aware if this is something specific to saddles or anything that has a stack size of 1.