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Oh interesting - thanks for pointing me to this. It's NOT the known issue with neighboring contour lines crossing when they have different topologies... looks like contours break with data to zero on a log axis. It works fine if I change the zeros to 0.1 for example.
See http://codepen.io/etpinard/pen/wWGOJw
First reported on http://community.plot.ly/t/possible-bug-intersecting-contours/633
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