The Naruto world indeed harbors many dark aspects that bring suffering and even death to its inhabitants.
In the Naruto world, numerous moments of perilous conflict arise, especially during times of war.
And naturally, there are plenty of moments that reveal the darker side of the Naruto world, dispelling any illusions of tranquility.
1. Children Trained as Lethal Assassins

Before the era of established ninja villages, wars between clans involved children. It wasn't until the formation of the village system that this practice saw improvement.
Although the second Hokage Tobirama established the Ninja Academy system for children's education, the final outcomes remain less than promising. This is because these children are trained to become ninja assassins.
Later on, privileges improved in Naruto's era. They could opt to become ninjas and undergo training before facing conflicts.
2. Chunin Exams Pose a Danger to Children's Lives

In the Boruto era, Chunin Exams have become more lenient, even with strict regulations to ensure the safety of participants.
But during Naruto's time, the Chunin Exams were a place where children aged 10 and above could face life-threatening dangers at any moment. Becoming a Chunin required the ability to make life-or-death decisions, putting young participants in perilous situations.
3. Human Experimentation Persists
In the era of ninja wars, regular humans find it challenging to coexist peacefully in the Naruto world. The reason being the existence of powerful ninjas, such as Orochimaru, who conducted experiments on humans. Despite being prohibited, these experiments took place in the shadows, claiming the lives of many.
4. Serious crimes go unpunished

This might sound illogical, but it's a reality in the ninja world. Unfortunately, those who commit serious crimes often escape severe punishment.
Perhaps these villains have turned over a new leaf, becoming kind and assisting the ninja alliance in war. However, it doesn't change the fact that they are serious criminals responsible for numerous heinous acts.
Take Orochimaru, for instance, who robbed many of their lives, or Kabuto, the instigator of the Fourth Great Ninja War, causing immense suffering. Yet, both are now only confined and allowed to do as they please.
5. Frequent massacres by a clan

Wiping out an entire clan with countless lives lost is a horrific decision, causing many to perish senselessly. Yet, this continues to happen frequently in the Naruto world. Notable examples include the massacres of the Uzumaki, Uchiha, and Kaguya clans.
6. Rampant discrimination and bullying

Discrimination and bullying remain persistent issues in the Naruto world since the story's inception. Even the main character, Uzumaki Naruto, had an unfortunate childhood, enduring isolation as the village shunned him simply for harboring the Nine-Tails seal. Heart-wrenching stories also include Hatake Sakumo, Kakashi's father, and the tragic tales of clans with unique bloodline limits, such as Haku's clan.
7. Village leaders and elders are the cause of all problems

The leaders of villages, especially those heading large ninja systems, often wield power that plunges many into misery or make misguided decisions leading to the villagers' unhappiness.
The leaders of old often harbored personal motives, leading to unnecessary conflicts or hesitating to make peacekeeping decisions, resulting in prolonged issues or conflicts.
For instance, consider the tragic case of the Uchiha clan massacre. While Danzo orchestrated the event, the third Hokage's delayed decision, Hiruzen, was a grave mistake. His slow response allowed the unfortunate incident with the Uchiha clan to unfold.