I haven't seen issues like that. There is a BOM tutorial here among other how-to videos: https://www.altium.com/circuitstudio/resources
Check if the missing items are in the displayed BOM before being generated in the output.
It helps to have a template that links into the BOM process so you can control the output appearance. I have attached a generic template that I use and you might modify as fits your needs.
Generic BOM CS Template.xlsx 15.0 KB