Sometimes in fanfiction, Molly sends Harry howlers because she's worried about him and wants to express her concerns strongly. Or it could be a plot device to create tension or conflict in the story.
It could be that Molly wants to get Harry's attention quickly and forcefully, and sending howlers is her way of doing that. Maybe Harry has been in some kind of dangerous or inappropriate situation.
Maybe she's trying to scold him for something he did wrong or to give him a stern warning.