Do the nails stick out at all when toe-nailing studs?
So long as one side of the heads of the nails are touching the studs, there is no problem. These nails merely keep the stud from slipping to one side or the other, and nails angled in from each side will do the job with no difficulty, even thought he heads are not fully flush.

If, for some reason, you had to drive a nail into the narrow edge of the stud (generally not a great idea because of splitting potential), the slightly protruding head might dig into the finish material. Not a problem with drywall, but paneling or wainscotting could be a problem. You could countersink the nail with a hammer or punch, but better to avoid such positioning.