I found this quote on a messageboard:
So it’s kind of left up to the reader.
This is the second time I’m having to say this: not ‘show’, 'imply that it may have happened.
It wasn’t the eyes at all. It was how they looked and moved. It just seemed like the animators didn’t have enough time/budget to spend studying how actual polar bears move, so they just did their best with how they thought they did, which inevitably edges towards some sort of uncanny divot, where you look at it and say “That looks sortof…off, somehow.”
The other problem was that we had “animals with human features” going on for a lot of the daemons - Pantalaimon had this the worst, where you had something vaguely ferretlike or whatever, but always capable of doing human expressions, which really, really just makes it look like some sort of creepy talking animal film. Ugh.
Oh, and I don’t even remember the supposed “off screen sex scene” so it couldn’t have been that important to the plot. Of course, pretty much all of the Amber Spyglass is a muddled blur in my head, so to heck with that.
I agree that the movie tried to grab too many of the plot elements from the books - the witches absolutely could’ve gotten dropped, for example - The BOOK was really quite compelling though.
I think this was rejected as being too much of a “downer ending”.