When Joe O'Malley and Patrick O'Malley are sitting together in the backyard, we see Patrick holding a beer. At the end of the scene, Patrick has no beer, and Joe is "ceremonially" handing him his first beer.
In the second swimming scene, Pete and Danny's swimming suits each change color. Pete's start out as blue, then become red, then switch back to blue, then back to red. Danny's start out as blue then change to green later in the scene.
When Mrs. O'Malley drives up to church with all the kids, after the car is parked and all the kids are out, a head pops up in the back seat and someone opens up the back door. On the DVD director's narrative, it is explained that this is the mother of one of the child actors who had been crouching down during the scene.