Downloads taking up double memory

I am downloading files and media off my time capsule through the 'file share' app. I open the files in the 'good reader' app but it seems the media is being saved twice.
I plug my iPad into my computer and the video and app size both go up. It now says I have 17 GB of apps when I clearly don't. How do I clear out the app memory and get rid of the media being saved twice?

In the iPad's operating system, iOS, each app has its own private file space. Any app that opens a file, has a local copy of it. However, the upside of this is that, if you don't need a file to be available any longer in a particular app, you can delete that file and the other copies will not be affected.

Tim