With any general 3D scan, it is very normal to see certain errors creeping into the scan. There are indeed few suggestions for your problem.
(a) Interpolation: Most of the 3D software interpolate data to fill the missing parts. But, interpolated data would never be as good as the original. So, we can help the software to interpolate data nearer to the original model by increasing the sample rate. This can be done by supplying it data from more number of perspectives.
(b) Lighting conditions. Since 3D scanning involves lasers and rendering of images, it very important to ensure that lighting conditions are appropriately maintained. Please refer to your user manual for the conditions best suited for your scanner