The unconnected fly line are expected as wired connectors or hard wires will make the finial connections. This is designed to fit in a tight spot ~ 1" high under existing hardware mounting plate.
5.0.1-4 is not up to date. You want 5.1.4 (currently at …-1 for Windows) to be fully up to date.
ERC and the BOM script you are running are done at the schematic level. The screenshot you took was of the PCB, and the check there is DRC.
For reference:
ERC = Electrical Rules Check
EESchema checks the schematic as best it can (w/o knowing the actual function of the symbols) if the schematic makes electrical sense based on symbol pin types.
DRC = Design Rules Check
PCBNew checks the PCB for manufacturability based on the supplied design rules which are either driven by the manufacturing capabilities of the board manufacturing process or special electrical and/or safety requirements.
The problem is that Python script is not prepared to handle reference IDs not of the form [A-z]+[0-9]+ when extracting the number. You could ask the author if this requirement should be relaxed, or change the IDs to conform.
I guess that is an advanced sort routine in python. Living with the obviouse renamed B+* to BP* sand B-* to BN* connector/jack references. The parts list then generated with no issues.