Intersection of two matrices- intersect function not working as intended
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I have two matrices, L1S (blue) and L2S (red), whose first 3 columns describe the x,y,z coordinates that I am interseted in. 

As I require the intsersection of these two matrices, (only the first three columns) I have used XY11 = intesect(L1S(:,1:3),L2S(:,1:3),'rows'). But the plot of the intersection, XY11 is found to have skipped obvious points of intersection. (See fig below)
I cannot possibly think of a reason as to why this is happening. I have never faced this issue before. Please note that the points coordinates in both the matrices are exactly matching at all points.
Any leads to the solution is deepy appreciated.
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