In The Spy Who Haunted Me, there's a strong hint that the Independent Agent's challenge is not what it seems, about halfway through the book. Supposedly, Alexander King had already investigated the five mysterious sites himself, and had uncovered the truth about them, but kept the information to himself. While this is plausible for cases like the Loch Ness Monster or the Appalachian mystery, it doesn't make sense for the Tunguska investigation: in that instance, it turned out that Eddie himself was responsible for the 1908 blast. There's no way that the Independent Agent could have discovered the truth to that story, because there was no evidence of the explosion's cause, prior to the novel's events; even if King had gone back in time to witness the original blast, he couldn't have determined its source from that, and a non-Drood couldn't have asked Grendel Rex about it without being destroyed for his trouble, either.
When William is dropped off at Drood Hall in Demons, the van driver makes a crack about having to transport an American mental patient and his giant invisible talking rabbit next. This seems like a fairly routine HarveyShout-Out at the time, but it later turns out that an actual pooka is looking out for William in the Library. Did the van have a stowaway on board, who was tired of hanging around the asylum with his previous companion?
The Droods dispose of their own dead by teleporting them directly into the Sun, to ensure that nothing remains of the bodies or torcs that potential enemies might make use of. This makes perfect sense, in a world where all sorts of evil Powers can exploit the dead ... except that in the Greenverse, the Sun itself is evil: the Serpent, sire of Nicholas Hob and arch-enemy of Earth (Gayle), as established in Drinking Midnight Wine. And we know from this Power's previous actions that using the dead as puppets is right up this particular villain's alley. Have the Droods been unwittingly handing their fallen kin over to one of the most powerful hostile entities in their Verse, all along?
Except that Drinking Midnight Wine doesn't exactly fit with the rest of the books. The magic and mundane worlds are split in that one which isn't the case in any of them. And none of Green's other books mention the Serpent In The Sun in any way. Especially since Gayle is really different between Drinking Midnight Wine and the Secret Histories.
Nicholas Hob has been mentioned in Green's other series, however. And while the full title hasn't been cited, the Serpentdoes get a reference or two. So Early Installment Weirdness aside, some of Drinking Midnight Wine is presumably still accurate.