Perhaps they are trying to avoid controversy. If the subject insinuated is a touchy or divisive one, ignoring it can be a way to keep the peace or not get involved in an argument. Another reason could be that they lack the understanding or knowledge about the insinuated subject and choose to ignore it rather than admit their ignorance.
One option could be to have a private conversation with the employee. Explain the importance of being aware of such underlying subjects and how it might impact the work environment or relationships. For example, if it's related to office politics or a team - building initiative that has an underlying message, the employee needs to understand for better cooperation.
Employers could create a more inclusive communication environment. If employees feel they can freely discuss stories and their implications, the problem of ignoring insinuations might be reduced. For instance, having regular team meetings where everyone can share their thoughts on relevant stories. This way, the employee who ignores the insinuation can be gently guided to see the importance in a group setting.
One possible reason could be a plot device to create drama. Maybe the author wants to show a rift between them for the sake of a more complex storyline. For example, if there's some misunderstanding or a secret that has come to light which makes Harry act this way.
The subject of a story is basically the main idea or topic that the story is centered around. It's like the core of the narrative that everything else ties into.
You could try to be more explicit. If you want them to engage with the insinuated subject, spell it out clearly instead of leaving it as just an insinuation.