Looking at this image:
You will see a blank space at the bottom. That's actually a disappearing app. Next to it you can see a folder that is missing the icon. Next to that you will notice a folder called PgAdmin.
Now, the missing app in the empty space is totally inaccessible. The folder with the name but missing icon might as well be. Clicking anywhere in those spots just acts the same as clicking in any empty space and closes Launchpad.
The PgAdmin folder I mentioned shows there are apps inside (the PgAdmin app and another folder.) When you open the folder, it displays as empty.
This happened while just trying to rearrange and organize launchpad. I'm using the most current (updated tonight) Yosemite.