Yeah, I've had a little bit of this just lately. After doing my lo-mount exhaust conversion recently, and having the whole tail-end apart, I was pretty sure I had snugged everything down but I lost a bolt from my Givi rack on my 600km round trip a couple of weeks ago, the one where I also picked up a puncture.
So I pulled the matching bolt and headed off to buy a replacement - no problem. Got home with the spare parts only to find, when I once again pulled the rear bodywork off, that the original bolt had fallen into the rear bodywork to one side of the seat, and had remained there all the way home. The shelf now has some spares waiting, should it ever happen again.
When I put the lo-mount ssystem on, I didn't insulate the struts which carry the weight of the muffler back up to the footpeg mount - I now have a few fibre washers in place there, and the vibration has been quelled noticeably, so I wondered whether I had actually slipped up on the tightening, or whether the extra bit of vibration did it.
Ages ago, I also dropped a mounting bolt off my Givi screen, and repaired it with some washers and an appropriate bolt....which is still in place, since Givi only do the whole mounting bundle, for $99.
I also had some trouble with my after-market footpegs for a short time, until I took the Loctite route with them...