Factual error: The train car in which Elle and the other passengers are held hostage is supposed to be an Amtrak type long distance railroad car traveling from El Paso to Dallas, yet on the inside of the car we can see a large poster showing the Washington, DC Metro system map.
Other mistake: When Morgan is showing the rest of the team the drivers license photos of the hostages on the train, every one of them is wearing the same shirt as they are on the train.
Character mistake: Close to the end of the episode, Dr. Reid says to the psychotic guy that was holding hostages, "M-theory cannot be proved." It should be "proven, " not "proved." Dr. Reid is supposed to be a genius, so he should be the last one to make such a mistake.
Answer: "The Boogeyman", s02e06. Spoiler alert: The kid is Jeffrey Charles and at that point he had already killed 3 other kids. Jefferey basically hated and resented other kids after his mother abandoned him and his father spent a lot of time with other children because of her job. Jeffery would lure kids Into the Woods and then beat them to death with his bat just because of hate, no particular "reason." The scene you're describing, Jefferey agrees to walk Tracy home when her "buddy" leaves her (at this point the FBI announced there's a serial killer on the loose and kids should walk with a buddy). Jeffrey gets mad at Tracy for walking too slow and for complaining, and he takes a swing at her, causing her to flee Into the Woods and have Jeffery chase her.
Bishop73