Here are the ones I can think of at the top of my head, but I'm sure there's more.
-The 'future' Screwdriver River has in "Silence in the Library" looking nothing like 11's
-Who's footprints were in Amelia's garden in "Pandorica Opens"?
-Who made the alliance in "Pandorica Opens"?
-Why was the Clara in "Asylum of the Daleks" called Oswin? In fact, why was the Victorian Clara's middle name Oswin when the modern day one had no idea about the name Oswin.
-Why was Clara's wifi password initialled "run you clever boy and remember (RYCBAR123)?
-Whos was the woman in the shop that gave Clara the Doctor's number?
-Why does the Tardis not like Clara?
-How did the Doctor and Clara get out of the Doctor's timeline when clearly in the episode the Doctor says once you go in you can't get out?
-What happened with the Human's and Zygons in "Day of the Doctor"?
Don't get me wrong I like Moffat as a writer. Before he was in charge of the series he wrote some great episodes. But as the showrunner, I think the thing with him is that although his story arcs appear better than RTD's, they either become poorly resolved or not resolved at all. The thing I l found most refreshing about Day of the Doctor was that it showed he is still capable of being a good writer, he just needs to stay with single, good stories and not keep leaving us with questions that will probably not be answered. I mean the whole "Silence will fall" thing was ridiculous, a nearly 4 year story arc which concluded as being just a sentence someone would say in 11's last episode which still doesn't really make sense.
-The 'future' Screwdriver River has in "Silence in the Library" looking nothing like 11's
-Who's footprints were in Amelia's garden in "Pandorica Opens"?
-Who made the alliance in "Pandorica Opens"?
-Why was the Clara in "Asylum of the Daleks" called Oswin? In fact, why was the Victorian Clara's middle name Oswin when the modern day one had no idea about the name Oswin.
-Why was Clara's wifi password initialled "run you clever boy and remember (RYCBAR123)?
-Whos was the woman in the shop that gave Clara the Doctor's number?
-Why does the Tardis not like Clara?
-How did the Doctor and Clara get out of the Doctor's timeline when clearly in the episode the Doctor says once you go in you can't get out?
-What happened with the Human's and Zygons in "Day of the Doctor"?
Don't get me wrong I like Moffat as a writer. Before he was in charge of the series he wrote some great episodes. But as the showrunner, I think the thing with him is that although his story arcs appear better than RTD's, they either become poorly resolved or not resolved at all. The thing I l found most refreshing about Day of the Doctor was that it showed he is still capable of being a good writer, he just needs to stay with single, good stories and not keep leaving us with questions that will probably not be answered. I mean the whole "Silence will fall" thing was ridiculous, a nearly 4 year story arc which concluded as being just a sentence someone would say in 11's last episode which still doesn't really make sense.
