The village elders or council could be the cause. They might see Sakura as a liability or not good enough for Naruto. So they manipulate situations to keep Naruto away from Sakura. They could send Naruto on dangerous missions alone or create false impressions about Sakura in Naruto's mind, which eventually leads to Sakura losing Naruto.
It could be Sasuke. If Sasuke has some sort of newfound connection with Naruto and it causes Naruto to shift his focus away from Sakura, then Sasuke would be the cause. For example, if Sasuke and Naruto team up for a powerful mission and their bond deepens in a way that makes Naruto neglect his relationship with Sakura.
Another possible cause could be a new character introduced in the fanfiction. This new character might have some special ability or charm that attracts Naruto. Maybe they share a common goal that draws Naruto closer to them, and as a result, Sakura starts to lose Naruto. For instance, a foreign ninja with a unique jutsu who needs Naruto's help and in the process, Naruto becomes more interested in this new person.
There's also the possibility that it's an accidental injury caused by one of Naruto's friends during a training session gone wrong. For example, Sasuke could accidentally unleash a jutsu that hits Naruto's eye while they are sparring.
A new, unknown villain could be the cause. This villain might have a special power related to mind control or mental manipulation. They target Naruto because of his status as a hero in the ninja world. By making Naruto lose his mind, they could throw the entire ninja world into chaos.
It could be Orochimaru. He is known for his devious ways and might manipulate Naruto into believing false things about the ninja world.
It could be the Hidden Leaf Village's council. If they were to unjustly accuse Naruto of a serious crime he didn't commit, like being a traitor, and try to imprison or execute him, that would surely make him lose it. He has always strived to protect the village, and such a betrayal from its leaders would be a huge blow.
Naruto could be forced to wear an embarrassing outfit for a day. Maybe something like a pink frilly dress, much to his dismay, and Sakura would get a good laugh out of it. He would be the talk of the village for that day.
Well, in this kind of fanfiction, it might be that Sakura loses Naruto because of a misunderstanding. Maybe some false rumors spread about her, and Naruto distances himself from her. Then Sakura has to find a way to clear her name and win back Naruto's trust. Or perhaps Naruto is influenced by some dark force that makes him turn away from Sakura, and she has to fight against this force to get him back.
One possible reason could be that she might have underestimated Naruto in the past. She often belittled his abilities and dreams, but as she grew and realized his true strength and determination, she felt the need to apologize for her previous behavior.
One possible motive could be jealousy. Maybe Naruto has achieved something that Sakura desires, like getting more recognition in the village. So, she decides to frame him to bring him down a notch.
It could be a new villain. A powerful and unknown enemy might target Sakura because of her skills or her connection to other important characters. This villain could have a vendetta against her specifically or be trying to send a message to her friends.
One reason could be that Naruto is focused on his own goals like becoming Hokage and he might see Sakura's feelings or her actions as distractions. He has a lot on his plate and may not have the time or energy to deal with her in a warm way.