are you using a scanner that is attached to an Ipad? I ve tried to recreate your problem with my scanner and programm and I don`t have this issue. I am using Artec Studio Program and and Artec Spider and Eva for Scan.
I believe that the problem is that your scanner isn`t merging together the different Frames that is capturing from the real model to create the digital model.
Check the parameters before you export the model from your programm. Maybe you will see something like split.
Solutions: Like mentioned above, before you go to Sculpt mode go to edit mode and remove doubles
Try another format. Like STL ( without texture or color info), PLY or VRML2.
Hope I helped