By default, the Reports section takes into account all the submissions ever received. When you delete entries from the Submissions section in your form builder account, they are not deleted from your reports. But you can update your Reports to mirror the content in your Submissions section.
Simply go to the Reports section of your form, select the report you want updated and press the Update Report link, on the bottom-right.
The report will then be updated and will no longer contain more messages than the Submissions table.