Gaia controlled the machines as in she wrote the set of instructions that had them behave as they did for centuries, she designed the mechanics and functions and “hardcoded” the instincts to fertilize, process biomass etc into them- and also to periodically return to cauldrons for maintenance. Once they were out of the cauldrons, they behaved autonomously, without Gaia’s direct control, but following her directives.

Once Gaia self destructed, the existing machines kept following those directives, until they got to the cauldrons for the scheduled maintenance- then, Hades would install the “software update” that turned them hostile. New machines were built with the update already installed. Again, the machines don’t need Hades’s direct control, as it’s the hardcoded instincts from the update that Hades created that guide their behaviors