Which Inkscape version? I did the original on Inkscape 0.91 by changing the groups with xml editor. 0.91 displays the svg correctly but I think Inkscape is up to 0.92.1 now and I haven’t yet upgraded. I’ve never seen Inkscape do something like that, did you by chance import and export it from Fritzing? The extra groups look more like the Fritzing import/export mechanism which appears to love adding groups although I’ve also not seen it add a second group like this.
Peter