That has probably happened to others as well, but I admit that’s something I didn’t know before running into.
In KiCad v6, when copying/pasting or duplicating symbols in a schematic (or across schematics), it will copy ALL attributes including the “exclude from BOM” and “exclude from board” ones.
Since there is no way to tell a given symbol has these attributes until you edit it, this is extremely slippery. I messed up a BOM because of this.
I have read that in v7, you could enable an option to show on schematic that a symbol is exluded from BOM, which is a nice addition. In v6, you’re pretty much in the dark.
One nice additional feature would be to be able to see those two attributes in the “Edit Symbol Fields” dialog. That’d be VERY handy.
Meanwhile, just be EXTRA careful.