I have no ideas for "resetting the counter" with regards to the Game Center since deleting the game and reinstalling it would clear the data.
Do you have every room type fully maxed out on upgrades? I don't yet am up to 53%. Those several characters over level 50 wouldn't happen to be Legendaries would they? I was levelling up luck on a couple of them and they wouldn't register for the challenge on Luck SPECIAL increase as it doesn't class them as Dwellers I don't think.
Easiest way to ID if the characters over level 50 is dweller or a legendary is on the collections screen.