I finally figured out what happened, the hoppers were in the auto smelter design.
C
C H
H → S
C ← H
C is chest
H is hopper with directions specified
S is smelter
The items I put into the chest on the top left ended up somehow getting put into the hopper above the smelter. Jammed the whole system.
I was thinking that too. I'll watch it to see if it happens again. Thanks