Here is a demo where there is a body in the root of the replaced subassembly. You see that that root is being moved but the child cylinder is left behind because it is not joined to its root by a joint.
Fusion has a user problem where this happens too often and we are working on how to address it. too often, subassemblies that are inserted are not fully connected by joints especially to the root component of the subassembly which often has no geometry. Until we make this more of a "default", you have to make sure to add a joint (perhaps just an as-built rigid joint) between root component and children.
In my demo, I did not add any joint in the referenced subassembly between its root and the child cylinder. I had the same result you had but the problem is more visible because the root has a body that is clearly moved.
The move component occurrence command that you used to create the position will move children along with the parent component being moved -- even if they are not connected by joints to that parent. This gives a misleading impression that there is a connection. This is part of the usability problem we need to solve. In the meantime: always make sure that components in a subassembly are connected in some way via joints, including the root. There is almost never a case where you want floating disconnected child components in a subassembly.