When a subtask is created under a parent task on a project, as of a recent update, it’s sort of “associated” with the parent task’s project but not necessarily part of that project as I understand it. Once you add that subtask to the parent project, it will list it twice (once in the project as a task and also under the parent task as a subtask). I’m guessing you have an automated rule or something going on that automatically adds it to the parent task’s project. If you want to remove it from that project so that it only displays under the subtask, go into the details pane of the subtask and click the small X to the right of the project.
