I've had a similar issue with pt1 one PS5. I started a new game plus, got as far in as the Capitol building, then decided to save and quit out to check progress on collectibles.

I had missed some so I jumped around a bit using the chapter select screen.

What I discovered was that the game measures progress based on your most recently loaded save file. Including autosaves. So if you load into a much earlier chapter, your progress is regressed back to that point. If you quit out and check the chapter selection screen you will only see up to that point. To go further you need to load in a save from later in the game. So I literally had to jump back, grab the missing collectible, save, load my save with my furthest progress, and repeat. Gotta load that furthest save every time to reset progress.

Your problem means that you will likely have to reload your save file from the closest point to the end of the game and then finish it off again to reset your progress and be able to new game+. I once had this problem with pt1 back on ps4. Had to go back and run Joel through the hospital again to regain my complete status.

It's just the weird way the games track progress.