It appears the EstimateNormals function does not work properly for completely flat patches, also somehow depending on the orientation.
To reproduce:
import numpy as np
import open3d
X,Y = np.mgrid[0:1:0.1,0:1:0.1]
X = X.flatten()
Y = Y.flatten()
pts = np.zeros((3, X.size))
pts[0] = X
pts[1] = Y
shape = open3d.PointCloud()
shape.points = open3d.Vector3dVector(pts.T)
shape.paint_uniform_color([0, 0.651, 0.929]) # blue
open3d.estimate_normals(shape, open3d.KDTreeSearchParamHybrid(radius = 0.5, max_nn = 30))
# show the shape
open3d.draw_geometries([shape])
If you write
pts[1] = X
pts[2] = Y
instead - it works as expected; if you use 0 and 1 or 0 and 2 as indices - it no longer works.
Expected:

Got:

Environment (please complete the following information):
Good catch. Looks like a numerical issue of this function:
https://github.com/IntelVCL/Open3D/blob/377fc7d6a47ea47681c25a1e07a5383d62a612aa/src/Open3D/Geometry/EstimateNormals.cpp#L40
I will dig into it when I got time.
Fun fact: adding minimal noise to the points fixes the problem.
Fixed in #1011