it might be possible that when you added the extra columns the CR/LF on that line might have been messed up..if you added all the extra columns needed ..i would say, open the CSV file in Excel format and then add an extra blank column to the end (using insert column to right in excel).. Doing that, will add an extra column to the end with correct CR/LF.. In SSIS, Source just select the columns that you need..
If this is a recurring process where the file has In Variable columns.i would suggest you to take a dynamic approach by using script task where you can split the data as suggested in link below , so that you don't have to do any changes to the file manually
http://agilebi.com/cs/blogs/jwelch/archive/2007/05/08/handling-flat-files-with-varying-numbers-of-columns.aspx