Adding productivity modules to a machine in a production block seems to unnecessarily multiply the number of machines when using the compute by factory option.
https://i.imgur.com/KBxaH63.png
As seen in this image, I have it set to calculate based on having 8 factories, but with the productivity module present, it's calculating based on having 16 factories, leading to a calculated rate that is double what it should be.
This coincides with the (non-default config) level 8 modules from Bob's mods, which I've configured to have 100% productivity bonus.
I'm not sure if this affects vanilla modules, but it's possible that it does.