The paper looks a bit funny: it is called "The likely cause of the EGRET GeV anomaly and its implications," but does not name the "likely cause" neither discusses the "implications." Yet, the paper does not provide any new information compared to the one published by Esposito et al. in "In-Flight Calibration of EGRET on the Compton Gamma-Ray Observatory", ApJS 123 (1999) 203. Undoubtedly, the EGRET is a very complicated instrument, but it is a very vague statement to say that (see Conclusions) "Although a detailed reanalysis of the calibration data is impossible at this time, we have shown that plausible systematic uncertainties in the calibration of the EGRET sensitivity for gamma-ray energies above 1 GeV can readily account for the universal anomalous excess flux." See also a discussion in Moskalenko et al. arXiv: astro-ph/0609768.
On page 2, the authors state "The pion production cross section at these energies is also very well known"
In fact, it is not. At low energies (proton momentum below 3 GeV/c), the data used are from 1960s and 1970s and the error bars easily allow a rescaling of the predictions by a significant factor (see plots in, e.g., Dermer, A&A 157 (1986) 223 or, better, look at the original papers referenced there). At high energies (proton momentum above 7 GeV/c), the scaling approximation is used. In the intermediate region, one can use interpolation (Dermer, A&A 157 [1986] 223) or event generators (e.g., Kamae et al., ApJ 647 [2006] 692). However, independently on the tool used they are all tuned to the same data from 1960s and 1970s so that the resulting gamma-ray spectrum does not change much; this does not mean that it is correct. See also a discussion in Strong et al., ApJ 613 (2004) 962.
On page 2, the authors state "as we will show, the anomaly is seen at all galactic latitudes..."
This has been known for more than 3 (4?) years, see Strong et al., ApJ 613 (2004) 962. The authors, however, state that it is their "new" finding.
On page 2, the authors state "The three dimensional cosmic-ray density for the latitude range |b| < 25 was derived from the Galactic plane matter distribution on the assumption of dynamic balance."
I can imagine that this model can give something close to the reality in the region where the pionic emission dominates (e.g. in the Galactic plane), but outside of this region inverse Compton scattering is an important player (e.g. Strong et al., ApJ 613 [2004] 962; ApJ 537 [2000] 763). It dominates the pion-decay emission at intermediate and high galactic latitudes. This means that the model gives a wrong description of the gamma-ray flux outside of the plane if the inverse Compton emission is not properly accounted for. The conclusion on the extragalactic background is thus wrong if based on such a model.
On page 3, the authors state "Any uncertainty in the self-veto correction would alter the sensitivity of the detector at energies above ~1 GeV"
The authors do not specify why exactly above 1 GeV. I think, the only reason for that is the discussed "GeV excess" which is observed above ~1 GeV. As I remember correctly, Alex Moiseev Monte Carlo simulations show that the backsplash is/may-be important near/above 10 GeV.
On page 3, the authors state "The all-sky pervasiveness of the apparent excess flux above 1 GeV energy (see above) strongly indicates that this anomaly is intrinsic to the detector."
I am not convinced that this "pervasiveness" points undoubtedly to the detector miscalibration. An existence proof without much of the discussion: there are, at least, two other interpretations of the excess, cosmic ray fluctuations (Strong et al., ApJ 613 [2004] 962) and dark matter annihilation (de Boer et al., A&A 444 [2005] 51).
On page 3, the authors state "We find that for different observations of these sources, there were variations in their measured fluxes in excess of 40%. Since the flux from these sources is expected to be constant, this suggests systematic errors caused apparent time variations over different observing periods. Thus, it is not safe to assume there are no systematic errors, especially above 1 GeV."
This is exactly illustrated in Fig 2 of Esposito et al. ApJS 123 (1999) 203 (the reference is not given). Yet, these sources and the diffuse emission itself were used to correct for changing spark chamber efficiency.
On page 3, the authors state "we are unable to explain the GeV anomaly as caused by any single systematic instrument effect that we have studied."
That already contradicts to the title "likely cause"...
On page 4, the authors continue "It is difficult to eliminate any of these possibilities, but no specific evidence has been found that they exist."
Okay, so we do not know the cause of the excess. Why do authors think it is instrumental? It can really be the case, but the data that we have do allow for other interpretations.
On the same page there is a discussion of the importance of EGRET observations to calibrate GLAST LAT. I doubt it.
Finally, if the EGRET excess is instrumental, how is it possible that the authors confirm the extragalactic background by Sreekumar et al. (ApJ 494 [1998] 523) including the region above 1 GeV ?