Ultimately, werewolves like Remus Lupin became second-class citizens in the Wizarding World.
Newt should have known that historically, putting people on lists does not end up well.
We don’t know much about this yet, but presumably Newt did this with the best intentions to help those afflicted with lycanthropy and protect others.
According to the ‘About the Author’ section of Fantastic Beasts and Where to Find Them, while working for the Department for the Regulation and Control of Magical Creatures in 1947, Newt came up with the Werewolf Register, a list of all the known werewolves in Britain.