Clips attached will hold videos of what was happening, but essentially, the Crusher wasn't able to export items from the first two slots. It wasn't able to do it from the first four at first, I cleared and replaced the whole system and it went down to three. Did that again and it was two. But didn't go down after another attempt. Don't know what is going on and I didn't have this issue with the Basic version of the Crusher factory.

Link to Inside Crusher vid since Github didn't take such large files

Link to system vid since Github didn't take such large files

Any chance you can send your world for testing?

What version of Mekanism is this? Also I don't remember but I believe auto eject only outputs one slot at a time, try using a configurator on the logistical transporter to set it to "pull"

Closing due to inactivity. I'm fairly certain this is related to this issue/FR, which has been implemented for v10. Let me know if you have any updates.