The song "That Episode of the X-Files Where Mulder and Scully Find the Little Girls with Their Eyes Burnt Out Because of Angels" by experimental rock band Technology vs. Horse is named for this episode, though its lyrics contain no references to the episode or even the X-Files in general.
The seraphim are described as having four faces; those of a lion, ox, eagle, and man. This is incorrect, as cherubim have four faces; seraphim only have one, which is covered by a pair of wings.
If to look upon the saraphim is to give up one's soul then why didn't Scully die when she saw it?
When Scully is performing the autopsy (the one where she sees Emily) there's a close shot of the dead girl. You can actually see her hands and head shaking, perhaps it happened because she was lying nude on a steel table, and covered only by a sheet.
If the Kernoff's were really devout Catholics why would they have waited six years to have Dara baptized?
Scully: I was raised to believe that God has His reasons, however mysterious.
Mulder: He may well have His reasons, but He seems to use a lot of psychotics to carry out His job orders.
Scully: As much as I have my faith, Father, I am a scientist trained to weigh evidence… but science only teaches us how … not why.
Scully: I've seen things. Things that have made me question whether there aren't...larger forces at work here.
Mulder: You know, they say when you talk to God it's prayer, but when God talks to you it's... schizophrenia. What is your God telling you now, Father?
Mulder: I know people in glass houses shouldn't throw stones blah blah blah, but that guy is paranoid!
Mulder: Look, Scully... I know you don't really want my help on this, but can I offer my professional opinion? You got a bona-fide super-crazy religious wacko on your hands.
The special effects of the four-headed angel weren't finished until literally hours before airtime.
The confession sequence that can be seen throughout the episode, was a last minute alteration as it wasn't in the original script. When the first cut of the episode came in, the producers realised that certain aspects of Scully's journey weren't coming through. Thus they decided to add an 8-page scene to flesh out the emotional journey that Scully goes through.
Mulder: Well, Scully, aren't you the Secret Squirrel?
Secret Squirrel was a Hanna-Barbera cartoon character, an anthromorphic squirrel secret agent who was a parody of James Bond (SS was Agent 000). Voiced by the legendary voice artist Mel Blanc, he was accompanied by his sidekick Morocco Mole His cartoon show debuted in 1965, four months before the fourth Bond film, Thunderball was released.
This was at a time where the Bond movies were reaching their first peak of popularity and had generated a host of imitators and parodies. The original Secret Squirrel Show only lasted for two seasons, then was rolled into the Atom Ant-Secret Squirrel Show, for another season. Since then, the character has been revived several times over the years as a "guest" on other cartoon shows.
Symbol: Four Faces
The four faces Scully sees on the "seraphim" are animals associated with the four evangelist apostles: Matthew (Winged Man), Mark (Lion), Luke (Bull) and John (Eagle). These animals are used in Christian art to symbolize these saints.
Symbol: Inverted Crucifix
Mulder refers to a crucifix hanging in what is usually considered an inverted position as being a "protest, a sacrilege against the Church". In Roman Catholic symbology, an "inverted" cross is known as the Cross of Saint Peter. Later in the episode Scully gives the correct interpretation, referring to a legend that when Peter was martyred, he asked to be crucified head down because he was unworthy to die in the same manner as Christ. Catholics have about two dozen different crosses with differing significance. Most laypeople are not aware of their different meanings.