In the TV show Fringe, which is completing its series run January 2013 at its 100th episode, there have been a number of mysteries revealed, and some never revealed to date. One of the mysteries outstanding is the presence of Agent Charlie Francis in episode S2E11, Unearthed, when he had been killed by the shapeshifter and his original body destroyed. Then that shifter itself was killed by Olivia Dunham in episode S2E04, Momentum Deferred.
At the time, I remember the producers explained that this episode was a one-off, a remainder episode from Season 1, and wouldn't explain how the presence of Charlie should be interpreted post-death. The non-satisfactory answer merely heightened the theory of a conspiracy worth watching.
For the Fringe mavens out there, seeing that this series is about the vaguaries of time and inter-universe travel, is there evidence built into any subsequent episodes that would have healed this continuity failure that I might have missed?