Calculus is one of those things if you are not doing it often you tend to forget its complexities.
As for the matter of energy conservation, it appears that energy conservation only holds in a local sense. What the article should say which it appears to have terminology wrong, is that energy is not conserved globally. If an early universe is sufficiently small enough then the dynamics are indeed localized. In this sense we would seek the Raychauduri equation to explain the strong local gravitational features - likewise, the presence of a curvature in the early universe may ensure that particle creation happens in an irreversible way which is actually another example of non-conserved energy processes which tend to be described by thermodynamic properties.
The problem with the idea that general relativity makes it that global energy is not always conserved, is a matter of consequence of the Wheeler de Witt equation in which the right hand side has a vanishing time derivative - the interpretation has been since that time falls out of the theory of general relativity as we come to understand it and the evolution is described by diffeomorphism invariances. However, taking that this interpretation is correct and we should do away with a quantum interpretation of time in the global parameters of our physics, we come along to find additional problems trying to describe the Friedmann equation since it is a general relativistic solution of the field equations ''that appear'' to be explicitly time-dependent (ie. the scale factor is time dependent and the scale factor is radius dependent).
Another way to view this, is that the universe is not fundamentally a classical system and even when it does ''get large'' there is still loads of quantum mechanical processes going on. One such feature we have come to accept is that the universe is getting larger, which means space is expanding - Sean Carrol has noted that the metric in such a way must change according to it's bulk energy. In a similar fashion, I have argued that the appearance of new space and time must mean additional energies, so the problem comes down to, why do we measure vacuum energy something of 10^120 magnitudes too small?
Well, what I have come to learn is that the vacuum energy hypothesis has been treated [incorrectly] - since the energy we measure in the observable horizon corresponds to on-shell particles. Zero point energy consists of what is called ''off-shell'' particles and these ''virtual particles'' do not obey the usual rules of energy and momentum. In fact, it is considered by many that off-shell particles corresponds to ''unobservable dynamics'' happening at scales which are far to small in both area and in time to be measured which renders them different to the usual matter and energy we encounter on a daily basis. In fact, these fluctuations are an example of many kinds of relationships of physics and relativity that are deeply related to each other. These ground state fields exist even when you remove all the visible matter and energy in a vacuum! This is what remains when you think there is nothing left! What is the residual energy, but other than the thing predicted by quantum mechanics itself, that space is not truly empty and never is truly empty since there is always a residual motion associated to the ground state of the field. Relativity calls it ''relative motion,'' that is, all things are in motion with everything else. In quantum mecanics, it is called the uncertainty principle, that is, there is no such thing as a true rest system and the thing we call rest is but an approximation - there is no rest system because as you will know, locations in space are subject to a complimentary law related to the momentum of the system. The same quantum motion is the motion attributed to the ground state. And as we learn from classical mechanics, that motion will generate a temperature - you could argue that open space shows us what this general temperature is as it is spread over space - since the vacuum is never at absolute zero, then the universe does posses a temperature, even in the so-called 'voids of space'' where hardly any visible matter or energy can be found.
I'd argue though, this is not a failure of relativity as is claimed in the article, but instead, a failure of our understanding of our physics. The Wheeler de Witt equation falls out of physics from a path quantization on the general field equations. The problem with doing this is that gravity is not even a real field from the prospect of relativity and so direct quantization will no doubt lead to some essential problems, some of those include:
1) UV Divergence, ie. Singularities
2) The Problem of Time
3) Conflicting theories
Certainly, it has been said for a very long time now that relativity and quantum mechanics are ''conflicting theories.'' This doesn't appear to be the case at all, only that our ''interpretations'' of the physics is conflicting, even right down to the discrete concept found in quantum mechanics compared with the continuous vacuum in relativity ~ recently it has been argued that something can be both discrete and continuous! So yeah, sorry for posting such a long post, I just love the sujbect of cosmic energy.