They were after your dog. Canines are very territorial, especially with pups in the den. If it had been just you, you probably wouldn't have seen them but they were gonna make sure your dog left the area. Most likely the only reason the pair didn't kill your dog was because of your presence.
I had a friend a few years back that was trail riding with his horse and dog and they got too close to a den. The pair of yotes followed them over a mile and it finally ended with a two on one rumble. His dog ended up with over 150 puncture wounds. Coyotes play for keeps! Its life or death in the wild and coyotes kill for a living. Pack heat and keep an eye on your puppy. Glad it worked out well though.