I think it's a much grayer area than you are making it out to be. There are situations where a single class needs to track its own state in a way that requires a hash of hashes or similar. If the internals are not exposed in any way, and the elements in the collection are pure data without behaviors of their own, then it's not really necessary to make those all into objects.

I have definitely seen people make the sort of mistakes you're talking about, and it always makes me worry when I see methods taking or returning complex data structures that are not objects, but I've also seen internal data structures that were objects for no real reason. Being able to ignore the internal data structure of other classes is one of the great boons of OO coding, even if the internal structure is something unusual like a hash of hashes.