To reproduce, in an inferior-python shell, type "a=[0,1]; a[0].[tab]", here [tab] means the tab key, no completion. In a terminal, the above procedure will pop up a completion list.
(python-shell-completion-native-get-completions (get-buffer-process (current-buffer)) "a=[0,1]; a[0]. ")
emacs -Qand seeing if it works. If it does, then bisect your Emacs config files.