Matplotlib draws markers centered around individual pixels of the picture, which means that actual marker coordinates are approximated. This is a considerable problem when smaller resolution plots are required (e.g. creating videos). In particular, markers with slightly different coordinates are displayed on the same position.

For MWE below, all six points have different ordinate values, yet it seems as if points 2,3 and points 4,5,6 have the same value.

MWE:

import matplotlib
from matplotlib import pyplot as plt

coor = [[0.5,0.525,0.55,0.575,0.6,0.625],[0.5,0.501,0.502,0.503,0.504,0.505]]

fig = plt.figure(figsize=(3.5,3.5))
plts=fig.add_subplot(1,1,1)
fig.subplots_adjust(left=0.01, right=0.99, bottom=0.01, top=0.99, hspace=0, wspace=0)

plts.set_xlim([0,1])
plts.set_ylim([0,1])
plts.get_xaxis().set_visible(False)
plts.get_yaxis().set_visible(False)

grph = plts.scatter(coor[0],coor[1],facecolor='k',marker='o',lw=0,s=25)
fig.savefig('test.png', bbox_inches='tight', dpi=100)

According to my visual experience, about two intermediate steps should be included so that the problem is no longer perceived.

The problem can be worked around by creating larger resolution plots and then downscaling them, which is sometimes a tedious process with bad side effects.

This problem was also reported on Stackoverflow:

http://stackoverflow.com/questions/43589568/increase-point-drawing-precision/

Best regards