That happens because of a bug in new versions of guake and there's a workaround for that in gnome that is described in the wiki and it worked perfectly for me in Ubuntu 16.04:
Ctrl' keybind problem:
As of guake 0.4.2-7 there has been a noted bug affecting multiple users concerning the use of the Ctrl key to toggle Guake window visibility (i.e. users that setup Ctrl+Shift+z to open the guake console are able to open it by just pressing Shift+z, independent on whether Ctrl key has been pressed).
To solve the problem you should manually fix the value of the GConf key
/apps/guake/keybindings/global/show_hide. Open a gconf-editor, navigate to apps > guake > keybindings > global > show_hide and replace
If you don't have gconf-editor installed (it's not installed by default in newest versions of ubuntu) you just need to install it by searching for it in the "Ubuntu Software Center" or in terminal using this command:
sudo apt-get install gconf-editor
Edit: I know there's already an answer with the same link but I've added a way to install gconf-editor and this way if the link dies, the workaround stays.