Another aspect could be that in some darker fanfics, if Bruce Wayne were to cross a moral line, perhaps Alfred would have to take more extreme measures. He might cut off Bruce's financial resources related to his vigilante activities. This would force Bruce to re - evaluate his actions and the way he operates as Batman. It's a way of punishing him to make him understand the importance of ethics even in his fight against crime.
There are also fanfics where Alfred withholds his support for Bruce's Batman activities as a form of punishment. Since Alfred is crucial in maintaining the Batcave, providing technical support, etc., without his help, Bruce would find it much harder to be Batman. This forces Bruce to think about his actions and make amends if he wants to get Alfred's support back.
Another form of punishment could be emotional. Alfred might give Bruce the cold shoulder, refusing to offer his usual words of wisdom or emotional support. This would make Bruce feel isolated and force him to reflect on his actions.
A really interesting Young Bruce Wayne and Alfred fanfiction storyline could be one where Alfred has a secret past as a spy. This could add a whole new layer to their relationship as he teaches Bruce some of his spy skills. It would be exciting to see Bruce adapt these skills in his crime - fighting later on.
The fanfiction often delves into the emotional connection between the two. Alfred is the one stable presence in Bruce's life. He is there to pick up the pieces when Bruce fails or has a setback. And Bruce, in turn, respects Alfred's wisdom and advice. In some fanfictions, Bruce might confide in Alfred things he wouldn't tell anyone else, like his doubts about whether he can really make a difference in Gotham. This shows the deep trust between them.
One possible reason could be that Bruce is being too reckless in his Batman activities. Alfred, being the caretaker, might see Bruce endangering himself unnecessarily and decides to punish him to make him more cautious.
Another possibility is that Bruce is making moral decisions in the fanfic that Alfred doesn't agree with. As Alfred has his own set of values and he has been around Bruce for a long time, if Bruce starts to cross certain ethical lines in the name of justice, Alfred would be disappointed.
One great fanfic is 'The Father - Son Bond'. It beautifully explores the complex relationship between Bruce and Damian. It shows how Bruce tries to be a good father while also dealing with his role as Batman, and Damian's struggle to fit into this new world with his own strong - willed nature.
One common theme is loyalty. Alfred's unwavering loyalty to Bruce is often explored in great detail. For example, in many fanfics, he will go to great lengths to protect Bruce both physically and emotionally.
One reason could be Bruce's increasing isolation. Alfred sees Bruce pushing away friends and allies in the fanfic. This makes Alfred disappointed because he knows that Batman needs a support system. Without it, Bruce is more likely to burn out or make hasty decisions that could have been avoided with some input from others.
Maybe Alfred is disappointed because Bruce in the fanfic makes some unwise decisions as Batman. For example, he might take excessive risks that could endanger his life or the safety of Gotham in a way that goes against Alfred's advice.