I just did a fresh install of 11.10 Desktop 64-bit. When trying to add some new application to the launcher weird things are happening.
The problem in the following: I tried opening a Terminal from the Dash. When the terminal icon appeared in the Launcher, I chose Keep in Launcher. Then I close the terminal. As expected the Terminal icon is still in the Launcher. So far so good. Now, if I open a Terminal using the Launcher, a second Terminal icon appears, and stays after closing. If I open Terminal again, a third will appear and so on.
The same happens with other applications that were not initially in the Launcher, but not with the original ones, like Ubuntu One.
Update: The problem can be solved by logging out and in again every time I add a new icon to the launcher. It's definitely a bug. I shall report it.
Update 2: Bug reported