Possible lethal uses of Shamal's and Yuuno's powers. Yunno can teleport people against their will. He did so to Arf in the first season and the Book of Darkness Corruption in the second. He could teleport you to the bottom of the sea and you'd die before getting to the surface (or simply be crushed by the pressure if deep enough). He could teleport you into solid matter or into the position of a human shield. And if he can teleport parts of people, he could teleport vital organs out leaving the owner dead or dying. And while Vivid 19.5 shows some Masters were kind, it is almost certain others were monsters, meaning Shamal probably has done such things. The fact that she didn't in the series can't be taken as proof otherwise because Hayate was giving her Knights the option of choice and any Master who would have given Shamal such an order certainly wouldn't have.
The history of the Wolkenritter. Were all their previous masters cruel? Or were there equally loving ones that the Book purged/altered their memories thereof?
Chapter 19.5 of Magical Girl Lyrical Nanoha Vi Vid indicates that some people were kind to the Wolkenritter, but until Hayate became their master, no one could overcome the curse.
In the final battle, all of the components are clearly parts from creatures we've seen defeated previously. Except for in the beguining, where an appendage looking like the upper torso of a human is making strange beastly noises...Until you realize thats probably the embodiment of all the people who ever succumbed to the book of darkness, screaming in terror, pain and despair...for who knows how many CENTURIES...
The extraction of a mage's Linker core is shown to be very painful, evidenced in multiple instances such when Vita was collecting pages for the Book of darkness from several TSAB agents, who were wincing in pain as their cores were collected, Fate passed out after her core was forcibly extracted and all of the Wolkenritter were screaming in agony as their linker cores were absorbed. Now just imagine what kind of hellish pain Nanoha had to go through when her linker core was assimilated, on top of being physically exhausted and beaten, while charging up and firing her most powerful spell, which, as we will learn in the 3rd season, puts a lot of stress on her body.
The use of what apppears to be a dead ringer for Admiral Clyde as the form for the Wolkenritter's Mysterious Protector becomes even more appropriate when you consider that Admiral Graham's familiars know Chrono is covering the case, and know about his father's death, potentially hoping to use it against him. After Chrono points out that their plan to deal with the book is illegal, Lotte tries to argue that following the law resulted in many people, Chrono's father included, dying before Graham silences her.
When the Book of Darkness started casting Starlight Breaker to get rid of Nanoha and Fate, Nanoha thought that they do not have to run as far away as possible. Fate corrected her, saying that they NEED to be as far away as possible as their shields would not be able to withstand the attack. This is because Nanoha has never been on the receiving end of her most powerful attack, thus has no idea how strong it really is. Fate, on the other hand, is the first person to be on its receiving end, so she knows exactly what to expect.
The roles of Admiral Graham and his two Cat Girls are axed in the movie version. This seems odd, until you remember that the movies are supposed to be TSAB propaganda. If they actually depicted the truth, the TSAB will be seriously compromised politically. This is a high-ranking TSAB officer conspiring to shove a nine-year-old girl from a neutral world into an eternally frozen void, and personally interfering with the TSAB's battles against the Wolkenritter.
The fact that the Masked Men's disguises as Fate and Nanoha were the wrong color is a huge clue to their identities if you're aware that cats are colorblind.