I think you are misinterpreting the report, as JMP is correct, I believe.
You want summary statistics for Data by Column 1, but with Data as a subgroup.
So, when you look at the report, the column labeled as
N(Data,Missing) is telling you the number of data points in the data column, when the value of Data is missing. Well, there are MANY missing values in the data column. But when the data column is missing, guess how many rows of data exist? That's right, ZERO. that is the number you are seeing.
Similarly, your columns labeled as N(Data, 0) will tell you how many rows have data when the Data column =0.
In my earlier comment I said that you would see the correct number of missing values if you specify the statistic N Missing. That column labeled as N Missing(Data, Missing) will give you the correct numbers because that will be the number of rows where the data is missing when the Data column is missing.
Sorry if this is confusing, but having a column named data can make that happen sometimes! I hope this helps.
Dan Obermiller