As Sekar mentioned above, that works. In addition I have found that by using:
replace(replace(replace([Column],CHAR(9),'',''),CHAR(10),'',''),CHAR(13),'','')
Replaces all of the carriage returns (which is what was causing my issue) with a single space. Thus when I paste into Excel, issue resolved. Originally I had figured out the CHAR(10) and CHAR(13) workaround when I start seeing it again :(
That's when I cam across the CHAR(9) workaround as well as the following information posted the other day on Microsoft Connect
Posted by JayakumarPanasonic on 3/7/2015 at 3:14 AM
IT IS A BUG AND MS IS STILL SILENT.
Yesterday whole day I spent to extract some data form SQL2012, where I faced same issue. Used CHAR(9), CHAR(10), and CHAR(13) to resolve it temporarily. Really surprised, why MS is taking this so lite and not fixed yet. It used to work fine with SQL2008. Give option SQL2012 configurable through: Tools | Options... or provide additional options, while pasting data in Excel.