Hello KBL,
If you have cameras from the both sides of the surface of interest, then the problem could be related to the alignment issues - if the cameras from each side are not positioned (estimated) accurately, the depth data from these two subsets may intersect and form the holes.
In case the image data can be shared with support@agisoft.com, please send the original imagery and the project with the alignment results that you are using, so that we could investigate the problem and try to find the approach to get better result.