Considering Eos hasn't been acting like a commander beyond vague 'do this thing' directives to specific individuals, I'm not surprised that the Machina are winging other at the moment. 

EDIT: Like, going back the only person to disobey a command from Eos is Lillian. And this is because she is the only one to actually get a direct command from Eos. The only other applicable thing that happened in the entire battle was when Eos told her people at the beginning to essentially kill people and defend the factory. And since the factory was basically indefensible from the get go, they're doing their best anyways. So claiming that the Machina fail because they're incapable of listening to directions that haven't been provided is incredibly misleading