The hook phases through branches and very thin geometry when going extremely fast, but that's barely an issue. The phasing you seem to experience is not a bug, the hook orbits the player when the full length is used and it looks like it phases through geometry when it's not even hitting it.
Don't blame the devs or the game for a lack of skill. Take your time, be patient and look around for better routes. I beat most of the sections hookless, so you should be able to complete them with the hook without an issue.