If your dataset contains instances with missing numeric values, BigML will ignore them by default when building clusters and centroids. However you can replace the numeric missing values with a default numeric value: the field's minimum, maximum, mean, median or zero.
In the dataset view, click CONFIGURE CLUSTER from the configure option menu and select your preferred option, as shown in the image below:
If you are using the BigML API, please read this subsection of the API documentation ("default_numeric_value" argument).