Comment 1 for bug 1252978

A solution is given at the very place:

;;;;;;;;;;;;

You might try toggling autoindent with

%autoindent

since I think that has caused the problem for me before.

You can change this permanently using ipython's customization. After the proper imports (see the link) the following should work in ipy_user_conf.py:

# Emacs sets the term to dumb so we can distinguish that way
if os.environ['TERM'] == 'dumb':
    ip.options.autoindent = 0

;;;;;;;;;;

Remains the question how to deal with this from python-mode.el