I installed now Python3-Jedi version 0.13.2 from Debian stable which seems to work. The error message is gone when I start Gnome Builder and I can auto-complete python methods. But for Gtk methods auto-completion still seems to be broken.
For example when I type:
button = Gtk.Button.new_with_label("button")
button.conn
I would expect that it auto-complete to button.connect()… but no method is suggested.