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.
To be fair, the servants all acknowledge that Colin was legitimately sick several times in the past, but often threatened to fall ill in order to get his way. The difference was usually decided by whether he was throwing a tantrum, or quieter due to actual weakness.
It's also fairly legitimate that their well-intended sheltering was making his disabilities worse. A modern physician may well have told them that living in a sterile environment was making him liable to allergies, and he needed physiotherapy exercises, not enforced immobility. (They still probably wouldn't expect such a dramatic cure, though.) And the point about his needing social contact and mental stimulation, however poor his health is, is perfectly valid.
Values Dissonance: In 1911, the British Empire was in full swing, and it shows in this book. Indian people are referred to as "blacks" and they're considered less respectable than white people. The narration even refers to Mary having used violence against her servants in the past.
Mary's abuse of the Indian servants, however, is meant to reveal that she is a spoiled brat. Martha also reprimands Mary for her racist attitudes when Mary becomes outraged after learning Martha thought she was "black" at first.
It's also quite clear that bringing up a small girl in the belief that she's inherently superior to those around her- even her caretakers- is what made Mary so dysfunctional in the first place.
On a less serious note, Mary, a ten-year-old girl, is often and bluntly referred to as "ugly" by both the narrator and other characters and often to her face. Also, compare the approving references to her getting "fatter" (i.e. healthier and less scrawny) with today's concerns with obesity.
Also, this: "She used the wrong Magic until she made him beat her."
More a case of Society Marches On, but we're supposed to see Mary- at least through Martha's eyes- as dysfunctional and hopelessly coddled because at the advanced age of nine she never goes anywhere by herself. In the same part of the world now, Mary would be at about the minimum age that children would start going out of sight of home without an adult.
Wangst: Colin is like this until Mary gives him a good talking-to.
The 1993 film and the anime series designate Mrs. Medlock as an overbearing caretaker, even though in the book her initial antagonism fades as the narrative progresses.
The musical designates Neville Craven, a doctor who wants Colin to die so he can inherit his brother's estate. In the book, he is in fact a deeply caring man who took up medicine to help his older brother.
Granted, it's not quite stated, merely implied by an accusation from Mary. He's still the primary antagonist, though.
The anime series not only does this to Medlock, but creates a character for this: Max Hawkins. He actually turns out to be a decent person once we get to know him, but he was badly broken in the past and thus he can't forgive Archibald Craven for his Break the Cutie experiences.
Die for Our Ship: The 1987 film has a bit of this outside of the story. Since the film makers made it so Colin and Mary aren't related, they had to get rid of Dickon. The only way to do that was to kill him.
The sequel to the 1993 version Back to The Secret Garden also does this; Dickon dies in the war between the two films and Mary and Colin end up married. The only difference is that they're still related in this version.
Nightmare Fuel: In any of the film adaptations, Mary walking through the house to find Colin can be deeply unsettling. The 1987 version takes this Up to Eleven with scary music and a lightning storm raging outside the manor — and let's not forget the cutaways to the light playing off of the dark, ugly statues.
There's also the opening from that same movie, where Mary's wandering through a house where everyone except her is dead or dying from cholera, and she doesn't even understand what's happening. Special mention goes to the lingering shot on Mary's dying parents, with their faces twisted up in pain.
Purity Sue: Arguably, Lillias Craven in the anime series.
The Woobie: The '93 movie gives us a dream sequence of a toddler Mary being abandoned by her mother in the jungle, and crying piteously. It's pretty heartbreaking.
The anime series gives us the Canon Foreigner Camilla. She and her mother were hated for being Roma, then her mother dies, later Lillias takes Camilla in as her lady-in-waiting and she falls for her young accountant Hawkins... and loses them both, so she has to leave the Craven's manor while being accused of killing Lillias since she got up the tree to get her a gorgeous flower as a birthday gift. She is epically broken, and it's a miracle she doesn't commit suicide or something and remains kind to Mary.