The following example (with Matplotlib 2.0.0b3) causes the colorbar inside the colorbar axes to be offset when outputting to PDF with a low DPI:

import matplotlib.pyplot as plt

fig = plt.figure()
ax = fig.add_subplot(1,1,1)
im = ax.imshow([[1]])
fig.colorbar(im)
fig.savefig('colorbar_test.pdf', dpi=7)

This wasn't an issue with Matplotlib 1.4:

and the bug was apparently introduces in Matplotlib 1.5: