Junior mentions it's his birthday while he's cleaning the pots at the orphanage. After "Uncle Marty" arrives at the house Junior says he'll be eight (years old) in two weeks. There's no way Junior can have two birthdays in between the orphanage and "Uncle Marty's" arrival.
All throughout the movie, Junior has all his baby teeth, and longer hair, and then looks a little older with shorter hair and a large top front tooth growing in. This happens within scenes, beginning in the orphanage.
When Ben is standing on the bridge watching the truck drive away with his wife in the back, he has the rifle in his hand. Ben and Junior turn around to walk back to the car and the rifle disappears. It seems unlikely he would have left it laying on the bridge.
At the last scene on the bridge, after Ben got shot, you can see the wheel of the overturned car turning in some frames and then be completely still the next, and then moving again a few seconds later.
When a piece of meat falls on Mother Superior, it falls on her nose and sticks to it. However, in the next shot, when she removes the piece, her forehead and her gown under her neck are also spotted. Then she takes Junior out of the canteen and her gown is clean, and in the next shot, it is dirty again.
When Junior crashes the car into the glass enclosure, while Ben is on the roof of the car, it's obvious that John Ritter has been switched out for a dummy, as evidenced by the stillness of the body, as the hundreds of tennis balls crash down on him.