Some notes:
Some have been mentioned in other comments.
Wood / stick automation can be scaled to game breaking levels in the thousands. The persists through prestige.
Several instances where the GUI fails to update when factory automation amounts are modified. The GUI may react in various ways. The product may stop growing but the materials are still being taken away. The product may be placed negative without a GUI update with product being subtracted and materials being increased. Worst is a combination of these where the product is stopped and materials subtract to nothing. Temporarily breaks the game until a save and reload is performed. This can result in several lost resources.
Cumulative effects surviving the prestige process. Not sure if this is intended to be a perk of sorts of if its a failure to reset variables.
Interesting Idea.. reminds me a little of kittengame.