I have been playing with similar issues: Gnome favorites bar was showing in activities view and dock was showing on lockscreen; as pomsky says, all of this issues are associated with the combination of Ubuntu Dock and Dash to Dock.
I found this workaround for customize the dock with almost all the options that Dash to Dock offers:
- Install Dash to Dock.
- Make all your customization.
- Remove Dash to Dock (from https://extensions.gnome.org/local/).
- Logout and login.
Although Dash to Dock was removed, the customization (position, size, behavior, appearance) persist on Ubuntu Dock and the issues (docks overlapped, dock shows on lockscreen and favorites shows on activities view) are not present any more.
Notes: with this method, the only thing that you lost from Dash to Dock is the "Dash to Dock settings" menu from the applications icon, and of course, the Dash to Dock settings entry in Gnome Tweak Tool. I haven't tried yet, but I think that if you make a change from Dock entry in Ubuntu settings, may be some customization realized with Dash to Dock settings will be lost.