Let's face it, the Time war is one of the biggest mysteries in Doctor Who, excluding his name.  Even after Day of the Doctor there's still a lot of missing info.  But there's still enough for plot holes.

9th and 10th Doctor said that he trapped Gallifrey, Skaro and any other planet involved in the Time War in a time bubble.  

First of all, considering how desperate the Doctor was to end it, there were a LOT of planets involved so about half of the universe probably just disappeared.  

Then 11 comes along and he's all like:  I watched as Gallifrey burned to the ground.

What happened to the time bubble?

And how does that play out with the Daleks?  Wouldn't they still be wandering around the universe?

And in Day of the Doctor, the 10th Doctor said that Gallifrey burned.

AND!

The Doctor (8.5) goes to destroy Gallifrey in a barn.  That barn is later revealed to be on Gallifrey.

Why would you go to destroy a planet while you are standing on that very planet!

I know he didn't have plans to survive but still, that's not the best plan.

-----------------------

I don't own the image but if I go missing, that's why.