It has got to do with the writing out of the nc files.
As you see from the error message, the variables have a size say xi_rho * eta_rho. The values you are trying to write to the variable has the wrong size. Either because it is being sent with the wrong dimension order or simply the wrong dimension (say xi_rho in place of xi_v).
Have you made any changes to the files that came with the download?
I have documented by experience with this in this post.
That should hopefully help you