I think it's either a Pokémon with sing or hypnosis. Yeah, the spore thing could work as well, but as someone stated: wouldn't the city be covered in dust?
It is most likely just hypnosis, but I have a hard time coming up with a way to explain how the grunt in Agate and Terra didn't fall asleep. The only thing I can think of that can repel hypnosis is insomnia.
At least with sing, they could repel it with earplugs. The song could be faint, so one barely hears it because it is carried around by the wind, but it is just loud enough to have you fall asleep.