Well, if you overlap phalanxes, then it´s your own fault.
I once had a Brutii army attack my city with onagers, the shot a hole into my walls and before my phalanxes(militia IIRC) could set up correctly, they got overrun by masses of romans, especially the charge of their general and their hordes of legionary cav broke the phalanx formation easily. sometimes the AI simply overwhelms your phalanx, especially with charging heavy cav. Didn´t play Rome that much lately though, so I don´t know how much heavy cav they field in 1.2.