When Evil Rin kills Majorin but doesn't die with her when the Queen says something about it, Shadow Hazuki explains that a Shadow continues living even when their Light Half dies. This doesn't make any sort of sense...until you realize that even a corpse still casts a shadow...
Evil Rin expresses a lust for the Queen that Majorin doesn't display. Seeing as Majorin and Evil Rin are connected in a way, this doesn't make much sense...until you realize that the Shadow Archetype trope is about a character who expresses what another character conceals/doesn't know about themselves. This implies (and eventually confirms) Majorin as having a crush on the Queen in this fic.
The loophole presented in Witches at World's End comes off as a convuluted Ass Pull. Even the other Shadows are confused about it...until you realize that Black Queen had read through the Book of Shadows and that said Book is established to have all of the Shadows' secrets. This would include the loophole.
The goal of the Shadows is to use a spell in the Book of Shadows in conjunction with the Seven Seals to set all Shadows free. However, it has been shown that the Shadows can leave their Light Halves at will, so why is this spell needed? The author, when called out on it, confessed to not giving it much thought when writing it.
Evil Rin (and later, the Queen) seem to prefer using melee weapons (a dagger and "keyblade", respectively). The fact that they're both Witches would indicate that they would prefer magic instead, but they don't. Even with Rule of Cool, this doesn't make sense in the slightest.
Shadows were established early on to be able to slip away when you least expect it, even during the day. Somehow, that went unnoticed for quite possibly eons before the fic even started. How does something that unusual go for that long without being discovered?!
It is explained in-fic that Shadows do not die with their Light Halves. Considering how many people are murdered or die from unnatural causes combined with the loophole presented in Witches At World's End, and we might just have more Shadows than Light Beings...several of which looking exactly like our deceased loved ones.
