I have been playing for nearly three weeks and my Hunter has yet to unlock all their skills. I have 1 point banked and 5 skills left to unlock. I've done every Adventure that rewards Upgrade Points, so my only way to earn points is through level-ups. I made sure not to spend any points between level-ups, so my math isn't off. As soon as I earned my bright engram I went into my skills and still hadn't earned a point. I've also started a Warlock, who I play less, but has still earned nearly all of their points despite only doing a few Upgrade Points Adventures.
Have you tried selecting the perks without the level up point?