Media overhypes a cautious plea for assistance made by scientists. Scientists receive their assistance, and announce that the discrepancy has been resolved. Media looks foolish, and claims the entire incident is indicative of flaws in the current state of science.

Good times.

Agreed. Everyone in the physics community pretty much knew that the FTL neutrino problem had to be a measurement error, including the group who published it. I think one individual had to resign because they jumped the gun a bit on the initial announcement, but overall they hit a situation with a pretty crazy and groundbreaking result and none of them could poke holes in it, and all of them were skeptical about it. They published that information in the most responsible manner possible, but the media handled it pretty poorly.

Some other cases are the first two "discoveries" of the top quark, which were both wrong (and the one in 1984 was by Rubbia who won a Nobel Prize for the W and the Z so he wasn't really a lightweight). Recently, CDF at Fermilab had to retract their W+multijet mystery which might have been a leptophobic Z' boson, but was just that they didn't understand their background (again, everyone kinda saw that one coming as well). Also a couple of the dark matter detectors thought they had some signal, but the recently announced LUX experiment negative results pretty much crushed them. This kind of back-and-forth actually happens all the time. That isn't bad science, that's just science.