I've noticed this too. I tried making the chariot just go "through" the units (i.e. click somewhere on the other side of them). This makes them go through the formation, but does not seem to hurt the ememy at all. It simply knocks them down and they get back up again. I chased a fleeing group all over the map for 10 minutes and was able to kill about 5 of them.

I've kinda of decided, unless I see otherwise, that chariots are bugged and worthless, expect archer chariots, for their arrows. I'll be disbanding them and sticking with calvalry for now.