He's a congressman from Florida, and he's been a thorn in the side of Kevin McCarthy ever since McCarthy tried to become speaker in the first place back in January of this year.
His main challenger is a man named Benny Gantz, who has sort of been a thorn in Netanyahu's side for a while now - right? - or at least his main rival.
So when we say something is a pain in the neck, we mean it's annoying or a problem, but not a big enough problem to prevent us from getting things done.