Dr. Teeth's eyelids/sunglasses have been bothering me for a while now, the way they fall too far down so that the pupils show up in the glasses area thus breaking the illusion that they are his eyelids.
Fozzie's gray eyebrows are very distracting and his head seems a little squashed and if you look closely, the gap between his eyes is a little too far apart.
Gonzo seems to have lost his manic eyes and reverted back to droopy sleepy eyes. If they widened more often, it probably wouldn't be that bad, but we haven't seen Gonzo do anything particularly of epic crazy proportions lately. (Aside from his one stint on the roof during the movie, that was the only time he seemed to channel pure Gonzo.)
I'm not happy with Sam's puppet, he was a lot more vibrant when his hair was shorter and his beak, his unibrow, and I think his head was narrower. And for the movie, his moving eyeballs could be smoother too.
Overall, I agree with the sentiment that the puppets seem a bit tame and dare I say stiff compared to the scruffy flexibility we see in the show. Maybe it's the high quality of filming that attempt to make the puppets bright.