To reproduce:

• Encode a pattern, set a high stack size like 100 rotten flesh to 100 leathers
• Put it inside an interface adjacent to the Chamber
• (Automate the Atomic Reconstructor using something like the comparator)
• Order the leather, all 100 pieces of flesh go into the chamber, ignoring the stack size limit
• Laser shot, and because one single laser beam can only reconstruct 37 flesh to leathers (300000/8000=37.5 rounded down to 37), you'll see 63 flesh left in the Chamber, bringing the automation to a dead end requiring a manual fix