Last I heard, the retest showed that all was normal. When making such precise timing measurements GPS has to be involved, which depends on satellites and Einstein's relativity (which is exactly the theory that was supposed to have been disproven here).
Because the satellites are moving in relation to each other and the ground and so forth there are other relativistic effects that affect measurements of time. Normally these do not matter, but with the precision required to measure such speeds we're talking about, they do. It seems extraordinary, but in the original experiment CERN forgot to account for this.
It turns out that the neutrinos arrived sooner than expected by exactly the amount that those relativistic effects would have altered the measurements. That is, 3 nanoseconds.
Looking around now, this has been the major criticism, but it doesn't seemed to have killed it, so perhaps there is something more. Still, cumulative systematic errors in an apparatus and operation the size of a country seems much more likely to me than a violation of physical law.
Because what we call the "speed of light" is actually the speed limit of the universe. Faster speeds are literally not allowed by physics. That light reaches this speed in a vacuum is more of a coincidence. The photon is a massless, chargeless particle that is its own antiparticle. Generally quite unique, and as a result of its properties when nothing is slowing it down (such as a medium or gravity) it simply leaps to the fastest speed possible.
Unless it does turn out to have some minuscule mass, in which case the speed of light is actually slightly less than c.
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