This is a mechanic/bug, a mechabug.
Before it was somewhat of a oversight to allow Skilled Traited players to hold onto their perk from level until level 7, which allowed them to pick both level 3 and 6 perks.
With new perk system, we enabled the saving of perk points such that you no longer lose em unless you use them but we remember what level you got that perk point at. So a perk you saved from level 4 will consider you level 4 when you pick your first perk no matter what level you are. That to me is working as intended and makes sense.
I'll change it back to what it was before for now since that's fair, but this will be changed in the future.