6. The Silence
A much bigger story arc than the rest on this list, The Silence have been a presence throughout Matt Smiths time as the Time Lord they blew up the Tardis creating the cracks in Series 5, all looking forward to stop the finale of Series 7 but they were most prominent in Series 6. The thing is, even though their ultimate goal (to stop The Great Intelligence from destroying the Doctors past and causing silence to fall) was seemingly reached on the second attempt (after blowing up the Tardis backfired), youd expect an ancient religion whod obsessed over this for millennia would actually double check theyd succeeded. If Id gone to the lengths of kidnapping a child from the most powerful being in the universe Id want to be 100% certain it had been time well spent. In the alternate universe the Silence was destroyed, but as that had Winston Churcill as the Roman Emperor we all assumed it wasn't real, implying the Silence and Madam Kovarian are still out there. I guess Moffat heard some of the complaints about the series serialisation and cut them out.
Potential Solution: The intelligent society went dumb and didn't check.