The warning message means that there is at least a Zero distance in your d distance matrix. This should be caused by at least two identical rows in your snp matrix (so the distance between them is equal to 0). In fact, the warning is given by the is.euclid() function and just is there to inform you that have two identical rows (and maybe you want to simplify them).

Are any of your samples identical? Do you have any duplicate samples (like negative controls with no taxa in them)?