Transparent objects cannot be scanned. One has to rub them with powder or something similar in advance. Still, the geometry is scanned then, but the object is no longer transparent.
Black objects reflect only little or no light and, thus, are unsuitable.
Very fine objects like hair or fur are too thin to be scanned.
For very detailled objects, it is not possible to scan all surface parts as the scanners are simply too large to get an insight into all of them..
Shiny objects are being distorted when being scanned.
Gerade Kanten are a challenge.
With very smooth surfaces that look alike the scanner looses the picture joins and cannot compose the images anymore.