I've got a whole host of questions with this module. While each individual encounter and characterization has a definite "cool factor", the overall module has many things that just don't add up.
The whole rationale behind the Queen's instigation of the plague doesn't make any sense. It's stated she wants to remove the Varisians, Shoanti, and poor. Yet this plague is non-discriminating, other than the fact that the poor always tend to suffer more, since they have no resources. It is an utterly chaotic and uncontrollable way to achieve her stated goal. There is no consideration made for stopping the plague from affecting everyone - in fact the Urgathoans imply that it should destroy the city, and have no plans of stopping at all. And that's another consideration altogether. The plague will doubtlessly cost the city immense amounts of money in terms of lost labor and trade, even if it is stopped at some point. This directly and seriously will impact the royal coffers, which are already drained. Considering the nautre of who the Queen is supposed to be influenced by (Kazavon), that also seems a very unlikely goal. Queen Ileosa is acting not like a scheming villain, but rather like a genocidal maniac - why?
The plan for the initial distribution of infection is also somewhat nonsensical. The blood veil is concocted in Korvosa itself, in the Urgathoan temple, and yet a mysterious ship is loaded somewhere else to sail to Korvosa for the express purpose to be sunk in the river, with the hope that at least some of its cargo washes up where it can be found in a timely manner. If the plague can be spread as simply as through infected coin, then spending huge amounts of money on creating a bunch of magic coffers, some of which may wash up on shore, is a huge waste of resources, effort, and unecessary exposure. Rather than providing a red herring, the plague ship is a clue, especially considering the papers knowingly left on it. There could be many other better plans for misdirecting the source of the contagion, while easily spreading coin throughout the city, in places and with people you actually want to target. In the module, there isn't even any way provided to follow up on the deposit of plague coins in Abadar's vaults - it's just something that has happened already.
The sudden appearance of the Gray Maidens is poorly justified. You cannot simply conscript all pretty women and la voila - there's a hardened, trained, loyal military force. Even assuming you can brainwash half of them, it makes no sense that the others aren't missed when they're imprisoned. Moreover, their equipment is seriously expensive, and takes time to make - where did it come from?
The Queen's Physicians are all petty rogues equipped with an expensive mask. Why? If their purpose is simply to observe and foster the spread of the plague, they are either hired help - which would not warrant a magical mask, or they are fanatical Urgathoans, which should have some appropriate stats.
The encounter with Vencarlo and Trinia is not really tied into the adventure in any way. I understand it is continuing the development of those characters, but if it is done here, it should have at least some purpose.
The vampire spawn encounter in Racker's Alley is also random, without any possibility provided of connecting these creatures to their source, or any added plot development.
The Lavender encounter seems incongruous to its effect. 700 people saved because you shut down a snake-oil salesmen? There've got to be dozens of such opportunists in a situation like this.
The Carowyn Manor encounter is a good example of a targeted attack, but unfortunately falls down on explaining how the attack was done. It implies that smokebombs with Vorel's Phage were used, but Ausio's description tells of crossbow bolts fired. So how did one intruder manage to fell every single person at that party? Nobody was able to defend themselves? Nobody could run away? That is just impossible without some serious other influence. If the smokebombs were used, what is their effect - it would have to be devastating? And does Jolistina still have 4, as described in her stats?
The Hospice of the Blessed Maidens was an Arkona warehouse. And so ...? This fact is thrown in there, seemingly important, but has no impact at all on the adventure.
The blood veil immunity of the Varisians is supposed to be a magical effect based on the influence of Vorel's wife on some Varisians, which is not necessarily by blood relationship, but rather through the Varisian "family". And yet the research notes are supposed to allow alchemists to find a cure based on this? That makes it mundane, and removes that whole interesting aspect.