So let's talk about the maybe most controversial in the whole series: Darkhaven
It's the episode, where the magic stuff comes into play.
I was watching season 2 for the first time, when I read about the magic in Watership Down. I really thought "What the...?" What a stupid idea. But then, the magic was mentioned already in episode 2.10 Mysterious Visitors. So, it's nothing that's really unexpected.
Now, we come to episode 3.08 Darkahven and Hannah learns the magic spell from Hedge. Because I think, the whole third season has only very good episodes (excepting 3.01 and 3.13, which are amazing), I really couldn't say anything bad about this episode.
The idea with the hedgewizard (or better Hedge the Wizard) is... let's call it unique, but it fits into the whole story. And it's good, that the creators did this step already here and not only in the second last episode. So even the end of the series isn't really unexpected.