For me, the biggest WTF moment is the dogfight/freefall. Suddenly, in the midst of a suitably gritty, Craigian flick, the Brosnan era is back, only with Moore-era FX.
This is where the Craig era jumps the shark and nukes the fridge. Come back, glacier surfing in DIE ANOTHER DAY, all is forgiven.
The freefall for me was big. He and Camille fall through the sky for a long time and go into the sinkhole or whatever you call it and then open her parachute. That's all fine and good I suppose, but as edited, right after they pull the rip cord, they are hitting the ground and surviving. According to the edits, the fall should have killed them. It would have been much better if we'd actually seen the chute open and them falling for a second or two before hitting the ground.
As it is, it reminds me of Tomorrow Never Dies where Brosnan's Bond and Wai Lin are escaping from a deeply sunken ship and reach the surface on a lone lungful of air, which is unbelievable. Raymond Benson's novelization had it better with the two of them sharing an air tank all the way to the surface.
The other WTF moment for me was Mathis being killed.

Mathis is not killed in Fleming's novels (or by the continuation authors) and it really pisses me off that they killed him in QOS, not to mention the dumb way the writers killed him off. Next to his MI6 inner circle and Felix Leiter, Rene Mathis is Bond's closest friend. I don't know if I've ever been as upset at an aspect of a Bond film than I am of this.