EDIT: my mistake, keyboard wasn't fully docked, causing these problems. Ignore this thread please :P
So I've found 2 issues (so far) with the mini compared to the full sized iPad.
1) keynote - there is no scrolling to the bottom of your work area (if your keyboard is up, you can't get down to the bottom of a page)
2) Facebook - when I click on a notification, and takes me to the page of the status/picture, the comment bar is at the bottom of the screen as usual, but if I click on it to comment, the keyboard covers it up
Post any issues you have found with apps on the mini