You should also pull your cavalry out of any prolonged melee - especially if it's with infantry. We've deliberately made them weaker in a standing fight (because they were!), their primary advantage was mobility. Charge, disengage, charge again is more effective than leaving them in a static fight.
There was a notification icon on the far left of the screen during the battle for an FM dying. I don't think you lost any, nor were there any other Seleukid FMs present, so he must have been killed.