Thank you for reporting this bug. Our development team is working to correct it in a future version of JMP.
The extraneous lines appear in the saved HTML output when there are excluded rows in the data table, or when using the data filter to filter the output. One approach you could take if you are trying to exclude rows is to make a subset table (Tables > Subset) with only the rows you want to use for the Control Chart, and create the Control Chart Builder output from that. Then, the HTML file should not display any extraneous lines.