Item conduits are pulling out the machine upgrades and unprocessed items. This happen's in both single player and server. The machines I used are SAG Mill and Alloy Smelter.

Chest (Ex-Green) --> SAG Mill (In-Green/Ex-Brown) --> Alloy Smelter (In-Brown/Ex-Blue) --> Chest (In-Blue)

When placing an upgrade in either machine they get pulled out and end up in the last chest. This also happens with Ore which mostly ends up in the last chest with only a small amount processed.

• EnderIO: EnderIO-1.9.4-3.0.0.35_alpha
• EnderCore: EnderCore-1.9.4-0.4.0.21-alpha
• Minecraft: 1.9.4
• Forge: forge-1.9.4-12.17.0.1936