This is when the challenge of applying the best strategy kicks in. You could have won by saving all your strong ground toons for offense to clear both zones, while still holding your fleet zone. If your opponent had to use multiple attempts on all but 2 of your ground teams, while you couldn't clear his ground zone, it seems like you set a too strong defense. If you hadn't then your strong fleet(s) would actually have won the battle for you.
You're penalized for using a weak strategy - not for having a strong fleet.