When you export a filter to Excel, if any of the fields have newlines in them Excel 2016 thinks that's the end of the field and the document gets all unaligned.
Incompatibility with Excel 2016.
- Open the exported CSV file in LibreOffice or any older version of Excel then 2016
- Please save the same file as a xls or xlsx file.
- Now try to open that file in Excel 2016 and should have no missing columns or row.