That article didn't even mention dark matter and dark energy. Those also "contradict basic physics" in the sense that they need to be conjured into existence to explain our observations.
"What’s more, there is an energy associated with any given volume of the universe. If that volume increases, the inescapable conclusion is that this energy must increase as well. And yet physicists generally think that energy creation is forbidden."
is regarding vacuum energy = dark energy = cosmological constant, etc, and continues to discuss it after that.
Another thing I find annoying is when they (this article and also others I have seen linked here on HN) paint the picture of that breaking energy conservation is some kind of magic going on -- it is far from it.
In General relativity (GR) you can construct conserved quantities from Killing vectors [1]. For example, if you have a time-independent metric (the GR tool for measuring lengths in space-time) you get a time-like Killing vector, which is associated to a certain conserved quantity; Energy. (Another example is when the metric has certain angular independences and you get conservation of angular momentum.)
Now in metrics that mimics cosmological evolution (that is, evolution in time), you have to break time-independence, hence your time-like Killing vector is gone and your energy conservation law is gone!
This is portrayed as some magic-like thing (at least that is how it sounds to me when I read these popular cosmology articles), but it is simply a consequence of the mathematics of GR. It might break some usual physics intuition, but I would not say that physicists (at least in this field) are surprised by it.
So it does not really "contradict basic physics", one just needs to know more about the details to get a good view of it. We do not need to figure out (or "conjure into existence") a way to break conservation of energy (as is the example here), it is already there in GR.
[1] https://en.wikipedia.org/wiki/Killing_vector_field#Geodesics The article on wikipedia is quite lacking on this point, but I link it here anyway.
> It might break some usual physics intuition,
It really shouldn't in light of Noether's theorem: The fact that time independence of the action S gives rise to energy conservation in the first place tells us pretty clearly: If your action has time dependence, you don't have conservation of energy.