You might have a PDF file that contains empty rows, like the ones highlighted here:

You can choose whether you want those empty rows to remain in your output file  (this is the default setting for PDF2XL):

Or, if you would rather remove them:

To toggle this option, go to Options > Conversion (or Excel) and find the "Keep empty rows" option.
Make sure it's selected if you want empty rows in your output; deselect it if you would rather remove the empty rows.

After you deselect this option, you will likely still see the empty rows in your preview, but your output should not contain any empty rows.