If the target creature is an illegal target by the time Settle the Score tries to resolve, the spell doesn’t resolve. You won’t put loyalty counters on a planeswalker.

Both loyalty counters must be put onto the same planeswalker.

You don’t choose which planeswalker receives loyalty counters until Settle the Score resolves. If you don’t control a planeswalker, you’ll simply exile the target creature and not put loyalty counters on anything.