A mundane cause for a surprising result. Consider this unconfirmed for now, however unsurprising it sounds.
According to sources familiar with the experiment, the 60 nanoseconds discrepancy appears to come from a bad connection between a fiber optic cable that connects to the GPS receiver used to correct the timing of the neutrinos' flight and an electronic card in a computer. After tightening the connection and then measuring the time it takes data to travel the length of the fiber, researchers found that the data arrive 60 nanoseconds earlier than assumed. Since this time is subtracted from the overall time of flight, it appears to explain the early arrival of the neutrinos.
New data, however, will be needed to confirm this hypothesis.
Source: Science/AAAS
I agree in general, but not as applied to this specific case. This is a major issue in science and/or epistemic rationality, about which prominent LWers have made bets, as noted below. News pertaining to "case studies" of this sort should always be welcome.