I'm using a 100 way Hirose connector in two places on my PCB (it's a Raspberry Pi CM4).  RPT labelled one connector as pins 1 to 100, and the other as pins 101 to 200, and with very different pin names, so the schematic uses two different footprints. But both footprints map onto the same part number so should create a single line in the BOM.  However the BOM generator doesn't recognise this and lists the part on separate lines, and hence creates a double charge for extended parts. I've also seen the same effect with other components where the footprint has needed tweaking for some reason.