Maybe he was poisoned. There are many villains in the Naruto world who use poison. If Naruto was poisoned during a fight or an ambush, it could lead to him coughing blood as his body tries to fight off the toxins. Just like how Sasuke was once poisoned and had to be treated.
One reason could be overusing his chakra. In Naruto's world, chakra is like life energy. If he overexerts himself and drains too much chakra, it can cause internal damage, leading to coughing up blood. For example, when he was training intensively or during a tough battle where he pushed his limits.
Well, it could be a result of a dark spell cast on him by a Death Eater. Maybe they found a new and insidious way to harm him without leaving an obvious trace.
One reason could be a hidden disease or affliction that is unique to the fanfiction world he is in. It could be something that has been passed down in his family magically. Or perhaps he has been in a situation where he was exposed to a harmful magical energy source for too long. This continuous exposure could gradually damage his body and result in coughing up blood. For instance, if he was trapped near a leaking magical artifact that emits harmful rays.
Another possibility is internal injuries from a battle. Fanfiction often has intense battles that are not part of the original story. Harry could have been hit by a powerful spell during a fight that caused internal damage, which then makes him cough up blood.
It could be due to a dark curse or spell. Maybe he was attacked by a powerful dark wizard using a forbidden spell that affects his internal organs and causes bleeding.
Perhaps in this fanfiction, Naruto is in a situation where he has no other source of sustenance. He could be trapped in a desolate place with no food or water, and the blood becomes a last - resort option for survival. This would be a very dark and extreme take on the character, as it goes against his usual values.
One reason could be extreme emotional pain. Maybe he witnesses the death of a very close friend or loved one in the fanfiction world. This overwhelming grief could cause such a physical manifestation as crying blood.
One possible reason could be some sort of dark curse or forbidden jutsu. Maybe Naruto was the victim of a malicious experiment that altered his blood composition. Another reason might be related to his connection with a dark entity. For example, if he has some link to an ancient evil, it could manifest in his blood turning black.
It could be a dark magic curse. Maybe some enemy has cast a spell on Harry that is slowly sapping his health, leading to him coughing blood.
In a Naruto coughing fanfiction, it could be a sign of a more serious illness. Maybe he was poisoned during a battle, and the coughing is the first symptom. His enemies might be trying to use this to their advantage, but Naruto, being the determined ninja he is, still tries to fight back while dealing with his coughing fits.