Using simple comparison to visualize overlap between two curves results in low overlap values being sorted to the end of the array

As found here: https://uk.mathworks.com/matlabcentral/answers/361760-area-between-two-overlapping-plots

I'm using a simple comparison to visualize the overlap between two curves.

y_d = [y2(y2<y1) y1(y1<y2)]; 

However, it seems as though all the sections with near-zero overlap (orange curve is on the order of 10E-7) are sorted to the end of the array, completely shifting the whole thing out of alignment.

I've realised that this method essentially creates two lists - the points where y1>y2 and the points where y2>y1, and then simply concatenates them together.

Are there any alternative methods that would conserve the relative positions of the points?