In boys, it is hitting puberty early and developing much faster than the other kids. On my kid's 2011 soccer team, there is a boy who is 5'5" and is very close to having facial hair. He is build like a 16 year old. If you put him on the track and had him run a 400, he would easily beat most 12 year olds who are very serious and compete on a high level in junior T&F. But I am sure by the time high school comes around and everyone else catches up, he will fade into the crowd as the advantage fades.
For girls, it can be the reverse. Pre-pubescent girls are string beans and have a very light frame, making them perfectly designed for distance running. Puberty for these girls can result in bigger hips, chest and more fat storage around the waist, hips and backside.
There are certainly other factors. A big problem with such a big focus on stratification in youth sports with national competitions, traveling teams, etc. is that kids reach a "been there done that" point with their sport and get bored and drop out. There was a study of elite soccer for kids under age 12 that found that kids who were in elite traveling teams under the age of 12 rarely went on to play in college or professionally. I think that kids in the junior high/high school age group have such a huge capacity to learn new sports and perfect new skills both in sport and other endeavors (art, music, drama, science, etc.) that confining them to one sport can be suffocating. And that may be why so many of the great athletes played so many different sports when they were in high school. Hyper-specialization can get a kid noticed at a very early age in sports, but it is not really a sustainable way to develop a great athlete.