There is a parametric nut trap on thingiverse if you are having issues. Pretty sure geodave made it.
I assume people have just been gluing them in like the tool holder nuts. I will double check but I think it says this in the instructions. I glue in the nut trap nuts and tool holder nuts, I saw this in the instructions yesterday but I will make sure it is in both places.
Sorry it a hassle for you guys, no has really mentioned it up until now.