I agree about James MacAvoy as Lord Asriel -- I really like him as an actor, but his physique/persona in that suggests more likeable, enthusiastic student geek than Pullman's dominating, fierce character.
Agree also about Timothée Chalamet as Laurie in the recent Little Women -- too pretty and spindly and emo boy-ish.
And though you can't really fault Kenneth Branagh as Gilderoy Lockhart, I felt in my heart Hugh Grant should have had it (his villain in Paddington 2 shows he would have nailed it). Likewise Bellatrix Lestrange should have been played (via time travel) by a young Jane Lapotaire.
(And Harry and Hermione should have been played by less stage-school-y kids, but that's not exactly controversial.)
Mark Rylance as Thomas Cromwell. He's brilliant, but too slender and cerebral. TC has to be a bluldog -- short, blocky and threatening-looking (as well as cerebral.)
On the other hand, some miscastings turn out to be strokes of genius. Though I realise about three quarters of my examples involve Simon Russell Beale, so that probably doesn't count, but a tubby middle-aged man cast against type as Hamlet and Ariel was just extraordinary both times.
He should be in everything.