Not sure if this is a bug or necessary for some reason I haven't realized.
Overlapping copper areas on the same net don't fully merge, unless they are connected by a *via - that is; both overlapping the same via in the same net.
*(via/pad etc.)
Examples:
--
![Copper area 1][1]
Highlighted: main GND copper-area.
--
...
![Copper area 2][2]
Highlighted: overlapping GND copper-area.
--
...
![stitched][3]
Stitched with via.
--
...
I don't think the stitching via should be necessary here..?
Browser:
Firefox 49.02 on Window 10
[1]: /editor/20161029/581493ae726ef.jpg
[2]: /editor/20161029/581494525a75d.jpg
[3]: /editor/20161029/5814949924e17.jpg