You have several physics objects that are not visible, because they are contained within the rigid body world collection but not within any other collection-- not even the scene collection. They are these three cylinders and three spheres, visible only after adding them to the scene collection:
![enter image description here](https://i.sstatic.net/NJECj.png)
As your linked answer offers, you can see the contents of the rigid body world collection in the outliner by switching the display mode to "Blender file" and looking in collections/RigidBodyWorld.
These objects (and many others) are multi-user data, perhaps giving you a hint about where they came from. The cylinders are parented to the spheres. Note that rigid bodies cannot be parented to other rigid bodies unless part of a compound collision body, and any that are may cause issues; there is an object "Body" that does exist in a visible collection that is parented and should not be (it is also constrained to its parent: the constraint is all that you need to establish the relationship.)
One way that this could happen is to manually remove the objects from their "real" collections. Generally when you remove an object from all collections-- like, remove from scene collection-- it becomes unlinked and is deleted in the next save/load cycle as orphan data. But because these objects exist in the rigid body world collection, they are not orphan data, and so even though there is no way of seeing them without some tricks, they continue to affect the file. Additionally, I would expect there to be high risk of bugs whenever using an object whose only membership is in the rigid body world. Many operations are likely to act under the assumption that things in real collections are the only things in the file. The "rigid body world" system is a weird outlier in how Blender typically handles objects and developers are likely to forget about corner cases involving it.
It's possible that you're in the habit of deleting objects by removing them from collections. That won't work when you're dealing with rigid body physics. Just delete them instead.