The one tooth is probably just coming in behind the baby tooth. He probably has a smaller than average mouth (not based on backtalk...lol) and so the permanent tooth grew straight down instead of at an angle. Once the baby tooth is out the other teeth will shift and the permanent tooth will move into place.
This happened to my daughter with a couple of her teeth.
Here's the only thing you need to watch for.... you need to be really proactive about your son wiggling his baby tooth. Since the tooth didn't grow on top of the baby tooth, it didn't grind down the root. So, he is, in effect, loosing his baby tooth LATER than he would have had the permanent tooth come in where it should. There will be a period of time where the permanent tooth has broken through the gum and is about 1/2 way in, but the baby tooth isn't all that loose. Food can get trapped in between the two teeth and he can wind up with a cavity on the front side of the permanent tooth. So he needs to brush really well and try to get the bristles of the brush in between the two teeth. You can also floss this area for him.
He needs to get the baby tooth out asap. have him wiggle it as much as you can every night. Not only back and forth but also side to side and in a twisty motion. The faster he can pull it the better. Try not to let more than a couple months go by where there are BOTH teeth in place.