Some commander decks have Planeswalker commanders. What happens when you put a +1/+1 counter on one of them, such as with Opal Palace?
Non-creature permanents can have +1/+1 counters on them, they just don't do anything until the permanent becomes a creature. Say you have a man land. If you animate it, then add +1/+1 counters to it, they stay on it even when it stops being a creature.
Also, cards like Earthen Arms can put counters on any permanent. Its gatherer says:
Any permanent can have a +1/+1 counter put on it. Those counters won’t have any effect unless that permanent is or becomes a creature.