This is me regretting not seeing this one before, but I actually know the answer here. This is because each power pole can only connect to 5 other power poles, and the Factory is powered like a power pole (to take power to another surface) and not like a machine (which you can use however many fit).
A single power pole connecting to two other power poles can't connect to more than three factories. This means that if you lay your factories out in a grid or a closely spaced line, you can very easily exceed this limit.
This is going to be fixed natively in Factioro 2.0.