This is contrary to my normal experience with Tableau. Tableau does not plot data where none exists. Can you attach a packaged workbook (.twbx) illustrating your problem? See Anonymize your Tableau Package Data for Sharing if applicable.
First, let's understand why Tableau plotted the areas on the map in the first place. You say "there is no data," but in fact there is data - there is a set of coordinates defining the polygon. That is data for that polygon, so it is mapped.
The field you have on color ([Size]) is from a different data source, and for that particular field, in the secondary data source, there is no data, so that field appears as NULL. To remove all the polygons with a [Size] = NULL, just drop SUM([Size]) on the filters shelf, select Special, and "non-null values." Your view will now look like your "good" image.
I hope that helps.
Because your follow-up question was unrelated to the original question, I branched it to a new thread.