So the general counteract rules use spell level or 1/2 creature level rounded up for things that are not spells.
" If an effect is a spell, its level is the counteract level. Otherwise, halve its level and round up to determine its counteract level. If an effect’s level is unclear and it came from a creature, halve and round up the creature’s level. " Core Rulebook 459
However there are a few examples where this is not the case.
First Example is the Clay Golem's Cursed Wounds:
"Cursed Wound (divine, curse, necromancy) A creature hit by the clay golem’s fist must succeed at a DC 29 Fortitude save or be cursed until healed to its maximum HP. The cursed creature can’t regain HP except via magic, and anyone casting a spell to heal the creature must succeed at a DC 29 counteract check or the healing has no effect. The golem’s counteract level is equal to its creature level." Bestiary 186
Another example of this is the level 16 rogue feat Dispelling Slice:
"Your sneak attack slices through the threads binding magic to a target. Make a Strike against a flat-footed creature (your choice). If your Strike deals sneak attack damage, you attempt to counteract a single spell active on the target. Your counteract level is equal to your rogue level, and your counteract check modifier is equal to your class DC – 10." Core Rulebook 189
So normally a level 10 creature (like a clay golem) would have a counteract level of 5 for it's abilities, requiring a successful counteract check with a level 4 spell, or a critical success from a level 2 spell. But as written it would take a success from a 9th level spell, or a critical success from a 7th level spell to counteract, which makes it essentially impossible for characters who are appropriate level to face a level 10 creature to counteract it.
Then suddenly at 16th level the rogue is the best dispeller in the game, having suddenly a level 16 dispel magic affect. (meaning successfully counteracts up to 15th level spells on a failure, though not on a critical failure)
I believe these examples are unintentional errors, but as written it could be quite detrimental to some play experiences, especially if they should come up in something like an Organized Play experience.
I first ran into this when our 8th level group fought a Clay Golem, and my fighter took 100dmg from 2 crits, and it became impossible for the group to heal him. The GM ended up giving us a macguffin to remove the cursed wound from some folks we helped.