8. The Duck Pond With No Ducks
When Steven Moffat took over as head writer he brought a different approach to overarching stories, not only lying clues but actually having the plots of earlier episodes directly link into (and often not make sense until) the finale. Some argue he went too far with the River Song/Silence sixth series, but the only time he really dropped the ball was in the very first episode of his tenure. There was always something off about Amy, as the Doctor kept repeating. It was eventually revealed the crack had claimed her parents, creating an odd, messed up world for her. But while that explained a lot of things that initially seemed off, theres still some elements in The Eleventh Hour that still dont make sense. When running around the small village Amy and Rory live in (living in London was
so Russell T. Davies), the Doctor makes a throwaway remark about there being a duck pond with no ducks. Given this is a disappearance, in the same way people have disappeared into the crack, many assumed it was directly tied into the series overarching mystery; the first clue in a deep mystery. But unlike other odd moments throughout Series 5 that didn't make sense (what the Doctor said to Amy in Flesh And Stone), this was never explained (or even mentioned again). Was it the crack in general or was it more directly related to Amy? We'll never know.
Potential Solution: The crack somehow took them.