When the rats visibly refuse to harm any of the dead servants or go near Hugo's room, this is a hint at him being the one who can control the rats.
Although he refers to himself as an alchemist, Lucas's research often seems less like traditional alchemy (the idea of using chemical reasons to transform one substance into another) and more like proto-chemistry. Although recognized today as a pseudoscience, research into alchemy did lead to discoveries which helped lay he groundwork for what is now known as chemistry.
In the second level, Amicia and Hugo visit a village populated by people who are at best indifferent to their plight and at worst actively hostile despite presumably being subjects of the De Rune family. Even if any of them liked the De Rune family, they're probably reluctant to help because they're afraid of the Inquisition. Mainly because if the Inquisition had reason to suspect a peasant of helping the people they're hunting, that peasant would probably be captured, imprisoned, given no opportunity to defend themselves, and be sentenced to a long and extremely painful death. Being a peasant in the Middle Ages is already hard enough, even if they were lucky enough to have a somewhat decent Lord in charge, and the Plague is only making it worse, so you can see why they might not be so quick to risk even more problems by getting on the wrong side of the Inquisition.
The Inquisition is probably not above taking advantage of the fact that most if not all of the peasants in the village are uneducated and illiterate to spread lies about the De Rune family and instill public distrust, so many of the villagers may have actually become afraid of Amicia and Hugo by the time they arrive.