Energy conservation just does not hold in general relativity (GR). It is replaced by Tuv;u = 0, where Tuv is called stress-energy tensor, but T does not include gravitational potential energy, because there is no gravity force in GR; there is only space-time curvature.
Primordial nucleosynthesis depends on how the universe was expanding during the first 3 min after inflation, which depends on how the energy density changed then. That energy is not conserved in an expanding universe is vital to getting the predictions of nucleosynthesis correct.
Energy conservation only holds on a static background with time-translation invariance. But in GR, space evolves with time. If we keep track of an amount of black body radiation, the energy per photon decreases due to redshift, however, the number of photons stays constant, and so the energy decreases!
Accelerated expansion is modeled by dark energy of about 10-10 J/m3. Dark energy is orthodox general relativity applied to the observed accelerating expansion of the universe! "Dark" means merely that it is not stuff that reveals itself by emission of light like stars do.
We get more and more of this energy the more the empty space expands. Energy is not conserved. Science never claimed that energy is holy juice rather than a constant under certain symmetries. Energy is Not Golden Holy Cow Urine (UPDATE: A post on that energy is not a substance and how to argue this easily is here.)
A nice reference on energy non-conservation in GR is:
Edward R. Harrison: "Mining Energy in an Expanding Universe." Astrophysical Journal 446, p.63-66 (1995)