It could be related to Molly's over - protectiveness. In the original series, Molly is very protective of her children and those she cares about. In the fanfiction, perhaps her protectiveness extends to Harry in an unwanted way. If she tries to control his actions too much, Harry, who is used to making his own decisions, might take actions that seem like punishment. He could restrict her access to certain information or areas that are important to the story's events.
Perhaps there's a situation where Molly makes a deal or agreement that goes against Harry's values. For instance, if she makes a pact with some of the darker forces in the wizarding world in an attempt to keep her family safe, but in doing so, endangers the greater good. Harry, being the defender of the wizarding world, would then have to take a stand against her, which could be portrayed as punishment in the fanfiction.
One possible reason could be a misunderstanding. Maybe Molly does something that Harry misinterprets as a threat to his friends or his mission. For example, if Molly tries to keep Harry from a dangerous but necessary task, Harry might see it as her overstepping and feel the need to 'punish' in the context of the fanfiction, which could just be a strong rebuke or some form of isolation within the story's plot.
One possible reason could be that she might think Harry is putting himself in unnecessary danger, like when he goes off on his own to face Voldemort without a proper plan. Molly is very protective, and she may feel frustrated with Harry's recklessness.
One possible reason could be that Harry breaks school rules in the fanfiction. For example, if he ventures into the Forbidden Forest without permission. Dumbledore is strict about the safety of students and such disobedience might lead to punishment.
One possible reason could be that Molly might blame Harry for putting her family in danger. Since he is often at the center of Voldemort - related troubles, her family gets involved in protecting him. For example, during the Battle of Hogwarts, her family was right in the middle of the fight mainly because of Harry. Another reason could be that she blames Harry for Ron's decisions at times. Ron follows Harry on his adventures and sometimes it puts Ron in harm's way, which Molly as a mother may not like.
One reason could be that the fanfiction changes her personality traits. In the original, she's kind - hearted but in fanfic, she might be made mean. Harry, who knows the real Molly, won't like this new version.
Another reason might be that Harry is suspected of sneaking around in areas where he's not supposed to be. Snape, as a vigilant teacher, may punish Harry to maintain discipline in the school. He may think Harry is up to something related to the ongoing dangerous situations in the wizarding world and wants to keep him in line.
In some fanfics, Snape might punish Harry because of his perceived insolence in class. Harry has a rebellious streak, and Snape, being strict, wouldn't tolerate any behavior that he deems disrespectful to his authority as a teacher.
One great Molly Weasley fanfiction is 'Molly's Moments'. It shows her behind - the - scenes efforts in taking care of the Order of the Phoenix members at the Burrow. Another is 'Molly's Motherly Love' which delves deep into her relationship with each of her children, especially during the tough times of the wizarding war. There's also 'Molly's Magic' that focuses on her underrated magical abilities.
It could be that in the context of the fanfiction, Snape believes Harry has been disrespectful towards him or other teachers. For example, if Harry were to talk back or show disobedience in class, Snape would likely punish him as a way to assert his authority.
He might give Harry detention. Harry could be made to clean the trophies in the trophy room or help Hagrid with some difficult tasks in the Forbidden Forest under strict supervision.
The relationship could start with mutual respect. Harry has always respected Molly as a mother figure in the Weasley family. This could gradually turn into something more romantic as they share more personal experiences. For example, Harry might confide in Molly about his post - war traumas, and Molly's understanding and care could lead to deeper feelings.