Corrected entry: Allan says Cory and Shawn have been best friends since Shawn taught Cory how to pick the lock on his playpen. But the flashback in "It's Not You, It's Me" shows Shawn and Cory meeting for the first time at the zoo, aged around 6 or 7.
Corrected entry: When Amy and Morgan enter Cory's bathroom, Shawn somehow gets out (presumably through a window). But in "Hair Today, Goon Tomorrow," the bathroom is shown, and there is no window.
Correction: Amy says that the door between Morgan's room and the bathroom is locked, so presumably, it is through this door and out Morgan's bedroom that Shawn leaves. There is a door there when we see the bathroom later.
Correction: He was saying that to imply that Cory and Shawn have been best friends forever, it was not meant to be take literally.