Who did Chigurh kill in the desert?

Although they're not named, they're clearly working for the same (also unnamed) criminal boss who contracts Chigurh and Wells to hunt for the money lost in the drug deal. We know that since they've been given a receiver to detect the transponder hidden in the case of money that Moss has in his possession, and because they're taking Chigurh out to the scene that they've already visited once before. I'm guessing these characters are permanent members of the criminal organisation, rather than guns for hire - on seeing their bodies later at the site of the shooting, Deputy Wendell makes one of his many hilarious observations, "These boys appear to be managerial" - although I suppose they could be private detectives or similar.

The most obvious reason for Chirgurh shooting them would be that he wants to make sure it's him who gets to Moss first and takes the money. However, it's also possible that following his initial conversation with them he perceives them to be incompetent, or just an impediment to his mission because he likes to work alone.

This is supported by later scenes when he shoots the Mexicans, who also have a receiver, at Moss's motel - and more importantly when he has a conversation about that with the frightened 'accounts' employee back at the office of the criminal boss, who he's also just killed:

Chigurh: "He gave the Mexicans a receiver."

Employee: "He feels... he felt... that the more people looking..."

Chigurh: "That's foolish. You pick the one right tool."

Chigurh sees himself as 'the one right tool'. Everyone else is either competition or just in the way, and thus expendable.

They are not named in the script.

POINT-OF-VIEW THROUGH WINDSHIELD It is night. No other vehicles on this paved road. Our car turns off and rattles over a cattle guard. Parked on the other side is a Ramcharger. Its passenger door starts to open. Outside: Chigurh emerges from his Ford. The man emerging from the truck wears a Western-cut suit.
MAN Mind ridin' bitch?

EXT. BASIN - NIGHT

THE RAMCHARGER Bouncing through ungraded terrain. It stops and discharges the three men-the driver and his partner, both in suits, from either side, and then Chigurh from the middle seat. They have pulled over at Moss's truck.

CHIGURH: This his truck?

He is opening the door and looking at the plate riveted inside.

MAN: Mm-hm.

CHIGURH: Screwgie.

The man reaches into a pocket and hands over a screwdriver. As Chigurh works it under the plate:

CHIGURH: -- Who slashed his tires?

DRIVER: Wudden us.

EXT. BASIN - NIGHT

A flashlight beam picks out the dog carcass.

DRIVER: That's a dead dog.

CHIGURH: Thank you.

Chigurh plays the flashlight around the scene. Dead bodies on the ground.

CHIGURH: -- Where's the transponder?

MAN: In the truck. I'll get it.

DRIVER: These are some ripe petunias.

Chigurh gives his flashlight to the driver.

CHIGURH: Hold this please.

He bends down and takes a 9mm. Glock off of one of the dead bodies and checks the clip. The other man is returning from the truck. He hands Chigurh a small electronic receiver.

CHIGURH: -- You getting anything on this?

MAN: Not a bleep.

CHIGURH: All right --

Chigurh stands and holds his hand out for his flashlight. The driver hands it to him. Chigurh shines it in his face and shoots him through the forehead. As the man falls Chigurh pans the light to the other man who has watched his partner drop. He looks up, puzzled, and is shot as well.

Later on, Wells is talking to a mid-level leader of the organization:

A beat.

MAN: He killed three men in a motel in Del Rio yesterday. And two others at that colossal goatfuck out in the desert.

WELLS: Okay. We can stop that.