My Model 3 was delivered August 6. I see that this issue of missing fasteners was started 2 months prior to my delivery. I, too, just happened to notice some missing wheel well liner fasteners, and found that I'm missing 6 of the plug-type push-in fasteners and 4 of bthe nut-type. I emailed the Seattle service center (Sodo) and the respondent said they checked three examples on hand and those were missing them, too. So it's now almost 3 months, and the same defect is still showing up. So much for correcting things at QA at the factory!
On a more serious note, I also noted that one rear wheel had snug-tight lug nuts. "Snug" is not acceptable on lug nuts. Of course, I checked the others, and they were OK. What do you think the chances are that the factory will be alerted?