If you are trying to create a 2.5D digital terrain model (a height field) from a point cloud then there might be two possible problems. Multiple points in the cloud at the same location don't add any information to the data, so are dropped. Multiple points with the same XY location but different Z location (height) are inconsistent with the idea of a planar 2.5D terrain model, and in this case
grid_terrain will take the smallest value of Z.
Repeated XYZ coordinates are probably not a problem unless you've got a lot of them, which might reveal that you've accidentally duplicated large amounts of your point cloud. In your case it looks like there's just four out of (I assume) a much larger number.
grid_terrain does the right thing. The internal
check_degenerated_points removes the repeats of identical XYZ points, leaving one point only at that position.