I'm assuming you mean where the vocal rejoins:
here
I'd always assumed it was shodding editing on the double-tracked vocal... If you listen to the vocal line, I think Nico may have had problems following a click track/ singing with headphones/ singing in general.
Though there's also a case to be made for it being intentional: at
4.40 or so the 'lead' vocal drops out a couple of times.
The unnatural beat I'm going to wager is a tambourine - hence it would've been on Nico's mic. I don't think Tucker used much in the way of cymbals.