How long is too long to cook meatballs in sauce?
That long time in the crock-pot sounds bad to begin with. Ground meat should be just cooked to a safe temperature -- any more and it will lose moisture and get tough.

The bitterness could come from prolonged exposure to the acidic tomato sauce. If you've ever made ground taco meat and over-seasoned it with lemon or lime juice, it will often taste bitter or astringent.