I'm making a scatter plot. Saving the figure in eps format makes (sometimes) a reproduction of the figure " show() " but the pdf changes (always) the configuration. For example, changing the colors and adding contour lines that weren't there.

Even worst in some cases saving the figure weather in eps format or in the pdf changes the figure itself.

fig2=plt.figure(figsize=[4,3])
fig2.add_subplot(111,yticks=[-4,0,4],xticks=[-10,0,10])
plt.scatter(X_l[:, 0], X_l[:, 1], c=np.array(colors[yy_lab].tolist()), s=np.array(sizes[yy_lab].tolist()),lw=0)
plt.axis([-11, 11, -4, 4])
fig2.savefig("fig.pdf",bbox_inches='tight',format='pdf')
fig2.savefig("fig.eps",bbox_inches='tight')
plt.show()