These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Hassam Bin Hassam from The Sleepwalker has habit of selling shoddy parts to airlines, which results in the deaths of nearly 350 people from a large plane crash, for which he had absolutely zero remorse. Hassam, when attempting to escape the country also murders his own wife and when cornered, holds his own son hostage with threatens to kill him if he is not allowed to go free. The same son Hassam had been seen to regularly beat if the boy showed any interest in Western culture. The same culture Hassam himself enjoyed without qualm.
Leonid Aramov, the Big Bad of the Aramov series, is the most vicious of the Aramov family and is introduced torturing Ingrid, a member of his own family, and tries to murder his own mother. He succeeds in killing one of his brothers. Leonid happily arms cartels and criminal organizations and regularly abused his first wife. His second prospective wife he beats, rapes, mentally tortures and threatens to kill their children should she try to leave him.
Designated Hero: James sometimes falls into this, though he usually gets called out.
Die for Our Ship: A canon example with Dana in The General, who is now cheating on her boyfriend to enforce First Girl Wins, despite the previous book showing him flat-out refusing to get together with said first girl because of how unstable it'd been.
Family-Unfriendly Aesop: You can make easy money by breaking the law. Cool People Rebel Against Authority. Friends let friends copy their school work. Slack off at school and cheat a lot, and you too can get top marks in your exams and go to the best university. Cool people don't care about school, and certainly not church.
As well as the above, those selected for CHERUB are naturally quite smart and do actually do their work, it just isn't the focus of the story, much like the lessons in Harry Potter in the later books. Ignoring the last bit as being religious shouldn't be considered an aesop. Oh, and they get punished for slacking off as well, or have you forgotten the Deadly Training Area or the laps?
In addition, most of the series focused on James Adams, who isn't that inclined toward schoolwork. Had it focused more on characters who are more focused on studying, then we would have seen more.
Romantic Plot Tumor: James and Kerry's relationship is this, with it starting off as an interesting enough romance that slowly evolves into a plot that makes you want to slam your head into a wall every time it occurs.
What Do You Mean, It's Not for Kids?: The latter books have "Not Suitable for Younger Readers" on the back of the cover, presumably because of the gritty portrayal of sex and sexuality, obscene language, violence, drug and alcohol use, adolecent bad attitudes, etc. Unfortunately it never specifies how young is "younger," and is marketed as a juvenile book.
The Woobie: Ethan Kitsell/Aramov. His mother was killed, his life was destroyed, his uncle Leonid is a psychopath and actively tries to kill him, and his only friend is a double agent.