Shadow and Bone, like most fantasy series, has some elements that weren't as well-thought-out as the rest of the story, and therefore just don't make sense. Some of these problems are because world-building can be difficult, especially in an adaptation. Certain things that were explained in the novel just didn't get included in the show too.
On the other hand, explanations for certain ideas are at least referenced or attempted, but fall flat on the screen. The explanation either wasn't clear or just didn't work, depending on the element of the series that didn't work in the first place. For example, the writers tried to explain how Alina suppressed her powers as a child, but it doesn't entirely make sense. So, what else doesn't make sense in Shadow and Bone?
Why The Testers Didn't Discover Alina
In the Grishaverse, the whole point of being tested for the Small Science is to be sure that you either have it or not. Alina is tested as a child but somehow isn't detected as the Sun Summoner. She manages to suppress her powers because she wants to stay with Mal, but more detail than that isn't really given.
However, it does beg the question, can anyone else do this? If Alina can suppress her powers, what's to stop someone else from doing it too to avoid being taken from their family for schooling and the army? It also implies the Grisha testers aren't as powerful as they first seem to be, which puts a dent in General Kirigan's idea of a strong, unified Grisha army.
What Does The Darkling Want?
As with certain villains, it never quite becomes clear what the Darkling wants to do, or what he plans to do with the world once he has it (since that seems to be his basic goal). Once he and Alina have all the amplifiers and he has extended the Fold further, then what?
He seems oddly resigned to being the villain, judging by the tone with which the Darkling says Shadow and Bone's best quote: "Make me your villain." It's almost as if he expected to be opposed by Alina and, later, Mal. Though his plan is to find them again to continue collecting the amplifiers, no one brings up the next plan after that, which seems like a strange omission.
Baghra's Motivations
Baghra's motivations are a little confusing. During the Darkling's flashback, Baghra is shown to be one of Shadow and Bone's most powerful characters, wanting the best for her son though she isn't willing to go along with his plan to create the Fold in the first place. Centuries later, she lives in the palace, but her origins have fallen out of collective knowledge. She trains Alina and knows that the Darkling is dangerous. Beyond that, what are the rest of her motivations?
Baghra does give Alina advice and help, but not much beyond getting her out of the palace. She's very much left in the dark as a mentor figure, and viewers will have to wait for the next season to see more of her.
Why Are Ravka And Shu Han At War?
This is a show-only element and it isn't as expanded upon as fans would like. Though the series makes it clear that the Fold has divided the world and that countries fight constantly over Grisha, it isn't really clear what the main issue is with global politics.
Why are Ravka and Shu Han at war, really? The audience doesn't even really know what event kicks off the plot of the series. Why are Mal and Alina in the army, other than it's customary that most people seem to enter it? Hopefully, further seasons will detail the reasons behind the conflict and the implications it has one some of the characters.
What Does The World Of Shadow And Bone Really Look Like?
The audience is given quick glimpses of maps, but there isn't enough time to really linger over one and study the way this world is laid out. Which begs the question, what does the world really look like? The series is either spent traveling across an unknown territory or inside a school's walls. The audience thus doesn't get a sense of the land.
Mapping out the characters' travels on a map would help for visualizations, as would discussing the different countries and what makes them different from each other. Both of those elements would help the Grishaverse countries really come into their own onscreen.
What Are The Amplifiers For?
The amplifiers seem to have one stated purpose: further strength for the bearer - as well as whoever shares that power, such as the Darkling, which is a key question answered in Shadow and Bone's first season. However, is that really all they do? Their differences in being from different animals should have some kind of effect, but it's never brought up.
The Darkling also never seeks out the amplifiers for himself. Is there any reason he can't wear them - that it must be Alina? It'll be interesting what happens with the next two amplifiers, and whether the series does anything different with them.
Mal And The Darkling's Fight
Considering the Darkling's sheer power and strength, it doesn't make much sense that his fight with Mal would drag on so long, or that Mal would emerge the winner. Especially considering all the other chaos happening onboard the skiff at the same time.
On the other hand, it is a human element to focus on in-between all the Grisha powers and Volcra attacks. The Darkling's loss also sets up his next move of creating his own shadow monsters. Regardless, he now knows Mal's weaknesses, which should change the outcome of their next fight.
Matthias And Nina's Relationship Doesn't Feel Important
As the third main plotline in an already narratively dense show, Nina and Matthias's story should feel important but fails to get itself off the ground. For one thing, it's made abundantly clear that the Druskelle soldier and Grisha healer hate each other, and always have. They work together to survive at first in the freezing cold, but later their relationship turns romantic. Matthias's furs certainly help and also shows off Shadow and Bone's intricately detailed costumes.
The novel uses the passage of time to spread their relationship out so that it feels passably realistic. The show makes it clear that everything happens during a shorter period of time, and the relationship's development falls flat. Nina and Matthias work well together towards the end of the series when everything between them is established, but their beginning doesn't make sense romantically.
Kaz's Fear of Touch
Kaz wears gloves constantly to avoid touching anyone or anything directly with his bare skin. Using his cane also allows him to swing things up to him instead of having to pick them up. This is explained in the novel, but not in the show, though the camera lingers over his gloves and cane more than once.
In the show, it simply seems to be a character quirk, but it is noticeable in some of his interactions with Inej. The show doesn't give an explanation. The answer is so deep in Kaz's very characterization that the only way it could be given is through flashbacks. The series wasn't quite ready to do that in season 1, but viewers can hope this will be elaborated upon in the next season.