Things that didn't make sense about The Time of the Doctor:
I guess my biggest disappointment was that the Battle of Trenzalore was depicted as an epic confrontation, with gigantic armies dying in a pitched battle: and instead what we see is the Doctor with a few villagers, holding pitchforks, and holding off an army of Daleks? For several hundred years.
We were also told that on Trenzalore, no one can lie or fail to speak (I believe). And yet the Doctor is being asked the question for several hundred years, and he manages to "fail to speak".
In The Name of the Doctor, we see the Doctor's grave, and a wrecked and growing TARDIS on Trenzalore. Neither of these seem to be possible, since the Doctor flies off, in the TARDIS, at the end of the episode.
River Song's grave was on Trenzalore, which requires some explaining.
The Silence, who were built up as a gigantic, mysterious threat, were dismissed as simply a renegade order of the Papal Mainframe.
The TARDIS exploding, which caused the Cracks in Time, weren't really explained.
The entire last story of the Doctor giving his sonic screwdriver to River before the Library seems to not be resolved, although it was hinted at in some mini-episodes.
I am pretty forgiving of continuity lapses if they don't ruin the story. Timey-Wimeyness is part of the deal. But I feel that a lot of stuff was done contrary to narrative logic: mostly that was built up as a gigantic battle where secrets would be revealed were just dismissed out of hand. "The scariest villains with a mysterious agenda that had the key to what was going on? Oh, just some unimportant, minor renegades"
Overall, I am a bit disappointed. I get the feeling that this was rushed through and that most of the effort was put into the 50th anniversary (which I liked).