Apps in Dock creating new icon
The issue is caused by Gatekeeper. It uses "path randomization" to run applications, until the user moves the app in it's final destination (/Applications for example). This causes the app to be run from /private/var/.. and Dock treats this as a new app.

To remove the quarantine attribute execute (removes recursively com.apple.quarantine):

sudo xattr -dr com.apple.quarantine /Application/SomeApp.app

Recursion (the -r flag) may be needed for apps that contain helpers.

To list the current attributes for an app execute:

sudo xattr /Application/SomeApp.app

or 

ls -l@d /Application/SomeApp.app


Sources:

On Gatekeeper and the Lifespan of Little Snitch Rules