@Bobby: Sorry, what you write is not about Refinement, it's about Global Fine Registration.
@Alex: Refinement is a Fusion option. Fusion creates a new closed mesh based on the original scans, with clean transition at the scan borders. The Refinement option tries to make the Fusion result more similar to the original scans. This is good when the original scans contain small details and align very well. If they don't align perfectly, Fusion can compensate up to a certain degree, but with Refinement it may cause the disturbances you have seen.
Since the algorithm cannot detect by itself whether it's better with or without Refinement, it is a user option.
I'm sorry, the user manual should give more info about the Fusion options... DAVID 3.9 will simplify the Fusion options a bit. We will then update the user manual...