Why did Pascal's guts come out so easily when Francis scratched him? You would only expect a few scratches. However, Pascal was repeatedly and cruelly experimented on. That also means repeated dissections and tuning up. That means Pascal's belly was especially vulnerable to injury, or coming apart. Even cats who haven't been tested on know to not expose their vulnerable underside.
This actually leads to a bit of Fridge Logic though. If he killed 400 cats and is so easily killed by a claw attack to the chest by Francis, why the hell is he still alive in the first place? Are we supposed to believe that among these hundreds of victims, not even one ever bothered to fight back? Sure, he had the element of surprise on his side most of the time, but he also talked to some of them before attacking them, and he also kills some of them in rather messy ways that don't exactly look quick. Are we supposed to believe that Solitaire just passively sat back and let it happen when Pascal ripped her open and cut Kong's the kittens out of her belly?
Imagine the horror the owner of Felicity must have felt when he walked in to discover his beloved pet cat to be brutally decapitated, knowing she couldn't have defended herself as well as a seeing cat? Worse, since many owners feel like pets are their children.
You see his reactions when you read that scene in the book. He's sitting in a chair, crying.
When funding ran out, the scientist began taking animals off the street. Some cats are indoor/outdoor. It's very likely house cats were taken to be tested on.
Poor Jesaja had the task of burying his murdered cat brothers and sisters, not knowing why they had all died, but knowing he had to try and put them to rest. And he was accused of being the murderer since he was at the scene of a cat who'd died. He was just a poor old cat trying to give some closure to his brethren.
Some of the members of the Claudandus Sect are kittens. There are children at a death cult meeting, which has and does happen in real life with humans. Hopefully, in the movie at least, the kittens and young cats are excused from killing themselves...? Even the best-case scenario, where the cats give themselves brain damage from electricity, is horrible. The cult wouldn't last long if all the cats killed themselves. The Claudandus Sect at least seems to have been going for a while, and Pascal seems to be at least 10-14 years old.
There's some discrepancy regarding the health of Jesaja compared to the Company of the Merciful, despite both being in similar situations. Both the Company and Jesaja live underground. The Company have gone blind from living in the darkness, but Jesaja has not. While Jesaja seems healthy enough with no sun, the Company have to sunbathe briefly every day to avoid getting rickets. It's never specified just how long Jesaja stayed underground, but the whole situation feels rather fishy.
Especially considering that cats actually can't see much better in the dark than humans can. They are also nearsighted, and it's mostly their whiskers (on the face, above the eyes and on the front legs) that do the work so they don't bump into things and so they don't go into spaces that are too small. Whiskers also help with hunting.
For a story wherein genetics and selective breeding play a big part, the art style of the film makes it hard to pinpoint the breeds of the characters (though in fairness, telling a cat's breed by sight alone in real life can be tricky in many cases, as they don't show as much structural variation as dogs), and the designs of some characters directly contradict the breeds given in the books.
Francis is probably a domestic short or mediumhair at least, while Bluebeard is likely a domestic mediumhair. Kong is probably a longhair, and perhaps also part bulldog. Felicity is a longhair Russian Blue. Hermann and Hermann have misaligned eyes, and crossed eyes is a trait many Siamese cats have. The Hermanns have yellow eyes, not blue, though it is stated in the book that they are Oriental cats.
Shouldn't Francis have found it somewhat suspicious that Pascal already knew about Felicity's murder so soon after it happened? You can chalk up his initial reaction to being horrified by the news, but even later on he doesn't question how Pascal learned of it.
Pascal does give the explanation that a stray named Agathe told him the news shortly before Francis and Bluebeard arrive at his house. What's strange is that Francis never asks to meet Agathe to confirm this story, and indeed we never meet her in either the book or the film.