
I will try to do this from most recent to oldest, and it is by no means comprehensive. This is just from the top of my head.
1-Soooo. We are to just brush of that apparently all the graves in the world are now empty??
2-no repercussions from a teen posting pictures from the moon?? While we are on the subject, recently there seems to have been an open door policy to the tardis.
2a-whatever happened to the kids that Clara nannied??
3-this one really bugs me...what was the deal with Clara's grandmother. A long story about a man in the fog and a ring, then no development from that.
4-whatever became of the big treaty between the Zygons and humans.
5-time lord relatives...River, Jenny and Susan.
6-10. 12's big opening quote of correcting mistakes he's made in the past, then nothing about his past beyond the first episode reference to dinosaurs in London and clockwork robot.
I'm sure you can add a few, some red herrings here and there are fine, but these are some big holes in a normally neatly tied together storyline. Maybe some will be resolved for Christmas, or we will get more passive aggressiveness from Clara and a Doctor acting like a jilted boyfriend. Think that may be the subject of my next article!