Even from a scientific point, there are other things in the universe that are not matter in the scientific sense. For example, there is empty space, there are forms of energy that are not matter. I'm no physicist, so sadly I can't explain this further.
But, from reading the author's comment that is not what the question is about. The actual question seems to be , if there is anything in the universe that exceeds the physical realm an goes over into a supernatural or metaphysical realm (please correct me if I'm wrong).
Well I have never heard of anything that seemed plausible to me, so I don't believe there is. But the problem with supernatural and metaphysical things is that they no more be proven than disproven.
At least not completely, we may be able to disprove any claimed miracle in the bible, or any other holy book, but disproving god is impossible, as he is, in his very nature, intangible.
You can not prove that an invisible unicorn doesn't exist, by saying you don't see it, hence it is invisible.
Another question is, why limit the speculation to our universe? Outside of it we have a totally different set of rules, so theoretically there could exist things that contradict the laws of our universe, and thus they would appear to be supernatural, but they aren't as they just follow another set of rules, which were still set by nature. The same goes for different universes then our own. Well I could go on about this for quite awhile, but in some way it would all just be wild guessing. So to sum it up, there could be and probably are things we can not observe, that exceed our understanding and contradict the laws of physics as we know them. But only outside our universe.
Everything is made of matter. Even air is not a blank space - it contains elementary particles that you noob chemistry students don't know about. Solid, gas, liquid, even animated, organic objects. Hello!
Only religious trolls would say that our universe have pockets of empty holes with no elemental particles.
Have we ever been able to isolate an aspect of the world, the universe, or existence that is supernatural and not still rooted in the physical?
We observe sub-atomic particles doing and behaving in extraordinary ways, yet these are still physical systems.
Metaphysical ideas: Love, Spirit, perhaps even Consciousness and Mathematics, etc., are still rooted in physical systems and bodies.
Does it make sense to be a Monist, concluding the universe is made of only one kind of stuff and it is physical? Or a Dualist, concluding the world has two aspects that are separate realities, the Physical and the Supernatural?
And if we want to think and believe there is a metaphysical reality, how can we say we have access to it and know that it exists when we are limited physical beings?