The issue was discovered here
deeptools/pyGenomeTracks#37

Basically, when fill_between encounters a NaN in the y values, when interpolate=True it produces a strange output.

This is without interpolation:

import matplotlib.pyplot as plt
import numpy as np

x = np.arange(107).astype(float)
y = np.append(np.zeros((100))+0.01, [0.5, 0.75, 1, np.nan, 1, 0.75, 0.5])

plt.figure(figsize=(20, 5))
plt.fill_between(x, y, interpolate=False)

If I turn interpolation on (which I wouldn't expect to do anything in this case, since there are not zero crossings), this is what I get:

plt.figure(figsize=(20, 5))
plt.fill_between(x, y, interpolate=True)

Even if I am misunderstanding something about how interpolation is supposed to work, clearly this is not what it should do...

mpl 2.1.2, python 3.5.2