The gun that Loki uses appears to be a Desert Eagle .50 caliber, however, every time he shoots it, it emits little more than a "pop" similar to perhaps a .22 or maybe a .38. A Desert Eagle .50 caliber pistol emits a very distinctive "boom" much closer to that of a shotgun.
When Loki convinces the Nun to take up an Atheistic lifestyle she is working/traveling alone. But even after Vatican II loosened restrictions on clothing and behavior, virtually every order still requires that their Sisters travel in pairs to forestall just such an occurrence.
In the Mooby headquarters, the glass that covers some of the posters (the Surly Duck poster in particular) is seen in some shots, but removed in others. (This was done to prevent reflections of the crew from being seen.)
When Azrael is holding Rufus, Bethany, Jay, Silent Bob and Serendipity hostage, Jay's positioning in the chair changes between shots. In several shots Jay is clearly seen sleeping, while in others he is looking at Azrael.
When Metatron first visits Bethany in her room it is clearly nighttime. Shortly after she turns on her lamp and stands next to her window, there are obvious times when the light is clearly coming from outside and others when it again appears to be dark outside again.
At the beginning of the re-dedication ceremony, the Cardinal is standing on the steps to the church and the trees are full of white blossoms. However, when the angels start to wreak havoc, the trees have their leaves. Clearly, this scene was filmed over several weeks... probably spanning late April to late May.
The Catholic concept of a Plenary Indulgence is incorrectly described. When Bartleby describes the Plenary Indulgence offered upon passing through the doorway of the Cathedral during Cardinal Glick's rededication ceremony, he states that by passing through the doorway "all their sins will be forgiven." Additionally, Grant Hicks describes plenary indulgence as a "clean slate." However, an indulgence is not the forgiveness of sins, it is the removal of the need for temporal punishment for sins that have already been forgiven through the Sacrament of Reconciliation, i.e. confession and absolution by a priest. The indulgence allows the removal of the need for punishment through penance in the current life, or through Purgatory in the world to come.
When Bethany is at Mass, the priest says, following the homily, "Let us now rise for the recession of faith." The correct wording is "Let us rise for the PROFESSION of faith," which is then followed by the recital of the Apostles' Creed. This was most likely done to satirize and/or draw attention to the idea that people's faith had faltered at the time the film takes place (hence "recession").
In the disclaimers at the beginning of the film, the word "judgment" is spelled "judgement". This is the UK English spelling of the word and is the spelling found in the King James Bible - it was clearly used for effect.
Protestants usually acknowledge that Mary was a virgin only until after Jesus' birth. Four brothers of Jesus are named in the Bible: James, Joseph, Judas, and Simon. However, Catholic tradition insists that these four (and some sisters also mentioned in the text) were children that Joseph had by a prior wife, thus maintaining the Perpetual Virginity of Mary. Since Bethany only knows Catholic doctrine, the news that Mary had other children comes as a surprise to her.
In the Mexican Restaurant scene, Metatron clearly said that angels can't drink alcohol because of Gods decree. Earlier in the scene, he quickly says "stop a couple of angels from entering and thus negating all existence" and immediately has a sip of tequila, it cuts to Bethany and you don't even hear him spitting it out, it cuts back to Metatron and his mouth is empty. Where did the tequila go?
At the end of the movie where Bartleby gets his wings shot off by Jay, just afterwards you see him brush two feathers out of his hair. Then they cut to Jay again, and when they go back to Bartleby you see him brushing two feathers out of his hair as he stands up.
Early in the movie it is stated that, as a result of Loki's actions, all angels were forbidden to imbibe alcohol. Toward the end of the movie it is verified that even Loki (and Bartleby) are still subject to that decree despite their banishment, based on Serendipity's comment about Loki's drunken state and it revealing he'd transubstantiated to human form. However, when Bartleby and Bethany are on the train talking, several EMPTY beer bottles are sitting on Bartleby's side of the table, while it is evident that Bethany's doing shots, not drinking beer. Bartleby couldn't have drank the beer due to the decree, but the spitting out of the beer (similar to the Metatron's tequila-spitting at the beginning of the movie) would have been a dead giveaway to Bethany of Bartleby's angelic nature. No containers are shown holding spit-out beer, so where did the beer go?
Rufus brings Azreal's gun with him when he, Jay, Bethany, Silent Bob, and the Muse head off to keep Loki and Bartelby from entering the church. Seeing how they cannot risk killing either angel, without undoing all of existence, and Jay is determined to use the gun, why bring it along in the first place, since they will risk doing what they are actually trying to prevent?