Something that has irked me for a while that I think really goes unnoticed is the organization of some of the monsters, mainly the outsiders.
I've seen Demons and Devils fighting alongside each other a few times through either summons or through a spawn and heard that Demons and Devils are fighting alongside and defending a Hag in Lysaga Hill. If that's true, why hasn't the Blood War started up in Barovia? You think the Dark Powers would take precautions against such a things. A Baatezu and a Tan'nari in the same room is trouble enough, but when you throw a Gehennen in there...that's just wishing for global annihilation. I haven't checked out Peridifus yet since my level 11 is too squishy to go there, but I've heard it has the same thing going on there too. My main, Anton, has seen this several times and flips out, thinking the Fiends are going to over take the place and murder everything. If the War ended up breaking into Ravenloft, I doubt even the Dark Powers could cool it all down. Even the Lady of Pain usually just lets it burn itself out whenever it breaks in.
Cranium Rats are another thing. I don't know if they are some kind of different breed or just a mistake on the DM's part, but Craniums aren't able to exist out of Sigil's Sewers. They require a gas emitted from a certain kind of fungus that grows down there to breath.
Maybe it's something worth looking into, or maybe it's just me being OCD, whichever it is...that's up to you guys.