This problem has affected everyone I work with that updated to the currently latest versions below. This only affects ipython plots. The regular python terminal is unaffected by this issue.
Reproduction
import matplotlib.pyplot as plt
plt.plot()
# manually close the window with `x`
Attempting plt.close() also disables the three native OS X window buttons
Workaround
Us the shortcut for closing ipython and then cancel the exit
^+d
Do you really want to exit ([y]/n)? n
Versions
ipython 5.0.0
matplotlib 1.5.1
OS X El Capitan Version 10.11.6
