Hello etnad,
If I understand the problem correctly, you have removed some elements of mesh that were between cameras and the area of interest, but it results in the fact that PhotoScan projects the original images on the existing surface, as it doesn't have an information that there is any "unwanted" area that shouldn't be projected on the available mesh.
So in such case I can suggest to mask the unwanted parts of the scene in the foreground on the original photos prior to orthomosaic generation process.