I remember a movie from when I was a kid about birds and beasts fighting to be the ruler of the animal kingdom. I also remember a vague subplot about a rodent or small animal going into a house. The animals were portrayed semi-realistically and not anthropomorphic along with owls and bugs playing a dominant role on the birds' side. The animals were definitely indigenous to North America. I'm pretty sure it is was made in the mid 80's to early 90's and it wasn't Secret of NIMH, Watership Down, or Silverwing though there are similar plot elements.

There was a Redwall cartoon that aired on PBS type stations a while ago... and I remember one of the stories specifically focused on birds battling the abby residents.