The end of the movie shows what is clearly a Roman Catholic funeral, presided over by the parish priest. Over the shoulder of one of the main characters can be seen a Masonic square and compasses on a tombstone which would be highly unlikely in a Catholic cemetery.
Fairuza Balk's tattoos are clearly visible beneath the make-up. One is a triangular shield on her upper left arm, the other is a circular tattoo encircling her right upper arm.
There is an altar allowing the priest to face the congregation. This change was not made until after Vatican II (1962-65). Until that time most churches did not have a free standing altar.
During the scene between Bobby yelling at his mom and Leon sending him out, someone (clearly not Bobby or Leon) casts a shadow on the wall.
Narration at the beginning of the film places the location as Sackett Street at Sixth Street. These streets are parallel and so do not intersect.
The neighborhood is continually referred to as Sunset Park. Even allowing for the location as Sixth Street, Sunset Park is on 41st Street, about 2 miles and several neighborhoods away.