Holes in mesh of 3D point cloud

I am currently simulating two interacting deformable bodies in Matlab. The location of all nodes of the two bodies are calculated by an XYZ point cloud. I am then attempting to mesh/skin the point cloud to visiuallize it's 3D shape. With all meshing methods I have attempted so far I get these small holes in the mesh shown here as white/gray stripes and squares. The position of the mesh holes changes at each time iteration. Has anyone had this happen, and if so, how were you able to remedy it?