clicking on the original icon should give you a new window?
this happened when i used netbeans and yandex browser.
should not be a bug, maybe it is the app itself.
just curious, did this happen to gimp in 2014.3?

Yes I saw this issue!
Also with Chrome and native apps..

Hello.
It still seems to be the same problem for certain applications like Google, Gimp, Spotify. When i used EOS i had found the solution here:
http://eos-snippets.blogspot.fr/2014/05/google-chrome-with-double-icon-in-plank.html
For Gimp, you have to open the Gimp application with a text editor in /usr/share/applications/gimp and change the line "Exec=gimp %U" instead of "Exec=gimp-2.8 %U". For me it's good!
I don't know the origine of this strange behaviour!

Thank you for your help jambalak, it works.

I don't remember this problem on 2014.3 but I haven't it anymore so ...
When I click on the gimp icon, the app starts and appears with a second icon in the launcher.

it happened to net beans and yandex browser on 2014, the issue still persist in 2015, however, starting apps from terminal did the trick.

Please upgrade the system, the problem is to be repaired.