Perhaps Naruto punishes Sakura for her hasty decisions. He could put her through a series of difficult tasks or training to make her more cautious in the future. This would not only be a form of punishment but also a way to help her grow as a ninja.
In some fanfictions, Naruto might punish Sakura for betraying their friendship. For example, he could distance himself from her, making her realize how her actions have hurt him.
One possible scenario could be Naruto being forced into a situation where he has to seem to betray Sakura to protect her from a greater danger. For example, he might be blackmailed by an enemy into staying away from her or acting against her interests.
Well, one possible plot could be that Sakura makes a mistake during a mission that endangers the whole team, and Itachi, as a strict figure, decides to punish her by making her go through intense training regimes. This would be to teach her the importance of discipline and caution in their dangerous ninja world.
Another scenario could be that Umbridge detains Hermione and makes her clean the classroom without magic. It would be a way to both humiliate and tire her out. Since Umbridge is known for her dislike of students who are too intelligent and outspoken like Hermione.
One possible scenario could be that Sakura is feeling down because she failed a difficult medical ninjutsu exam. Naruto, being the good friend he is, takes her out for her favorite ramen and tells her stories of his own numerous failures and how he never gave up. This cheers her up as she realizes that failure is just a stepping stone to success.
In some fanfictions, Snape might punish Ginny for misbehaving in Potions class. For example, she could be given detention for accidentally causing an explosion during a brewing experiment.
One possible scenario could be that Sakura makes a mistake during a mission. For example, she might disobey an order which endangers the team. As a result, her punishment could be extra training sessions led by Kakashi. Another scenario might be that she accidentally reveals a secret. In that case, she could be punished by being restricted from certain important village activities until she proves she can be trusted again.
Sometimes, in these fanfictions, the punishment is related to a competition. Say there's a magical tournament or a Quidditch - related event where Draco believes Harry has cheated or played unfairly. Draco, being the proud Slytherin he is, decides to punish Harry. It could involve making Harry do embarrassing tasks or even trying to get him banned from future competitions.
One possible scenario could be in a fanfic where Sakura accidentally uses her strength during a training session with Naruto and physically hurts him. Maybe she misjudges her punch or kick.
One possible scenario could be that after a long and difficult battle, Sasuke realizes how much Sakura has always been there for him. In a moment of vulnerability and newfound appreciation, he leans in and kisses her. It's a kiss full of unspoken emotions and a new beginning for their relationship.
In some fanfictions, Sakura might confess to Naruto in a very emotional and private moment. For example, perhaps after a dangerous battle where they both almost lost their lives. She could pour out her long - hidden feelings, saying how she has come to truly see Naruto for who he is and not just the annoying kid from before.