I don't know if this helps, but we have two puppies who are now 10 months old. When they were younger, one of them socialised well, but the other used to yelp at the sight of another dog, a person, a car, anything - as though it was going to be murdered where it stood! And if the two pups were playing, the same one would yelp as though the other had bit its' leg off or something. Now though, a few months down the line, there is no problem. Our little yelper has got her confidence and is fine in most situations - she certainly doesn't yelp any more.
So, maybe it's a little to do with a confidence problem, on top of the fact that your two are probably trying to sort out their own pecking order!
Don't worry, I'm sure as time goes on this will resolve itself, especially if you have them neutered.