That is likely an artifact of the rescaling (possibly due to rounding). After a rescale circles are often an ellipse with an rx and ry rather than an r. My script looks for that in the pcb svg (but not the others) and flags it as an error because the gerber output won’t create a hole for an ellipse. In breadboard or schematic it usually isn’t an issue.
I’ve not seen that documentation, it may be for an older version (much of the documentation around is). All I’ve ever used for buses is a bus definition in the fzp file which defines the bus name and specifies which connectors are in this particular bus. The check script checks to make sure the connectors exist in the svg, but I’ve never had to put them in a special group (and the current parts file format document doesn’t specify any groups needed) and usually leave them in the layerId group. The new parts editor internal connection feature creates the necessary buss definitions in the fzp file. If (as in this case) the pins are connected together internally to the board, then they should be bussed in the fzp (or via parts editor) so the nets come out correctly.
Peter