How, the clouds are super sparse (are you using subsampled core points or are the clouds super sparse? If you are in the first case, you could use all the points). And then they are also quite noisy ;)
And last, how are the normals? All properly oriented? (it's hard to see).
Issues with M3C2 cloud comparision
Re: Issues with M3C2 cloud comparision
Daniel, CloudCompare admin