Because for some x,y points you have multiple values For example your first two data points are both for -0.03, -0.02. I’m not sure what you want to visualize, but you might need ListContourPlot3D or a dimensions reduction.
Yes, I know. These are some Mesh Points and I just wanted to see them without the value assigned to them. The Documentation does not say that all {xi,yi,} values must be different, so I assumed ListPlot3D has the built in intelligence to display minimum one zi value for the many same xi,yi points.