In chapter 1 near the large river, there's a man with a shovel fighting 3 nekkers.

These nekkers will not die - hitting them, igni-ing them, trapping/bombing, etc. does no damage to them.

Are you using your silver sword?

If you approach the nekkers by climbing from the river, yes they're invincible. (happened to me)

Go towards the town using the path, and then go back, and they should be defeatable.

Exit the game, start it up again and try again. Maybe save at the city then get back there. I guess it's just a random bug.

From what anticitizen101 says, it sounds like they're using a area trigger to unset their invincibility so they don't get killed or kill before you reach the encounter, and not so much random.