If you filed your 2011, 2012, and 2013 IRS taxes late around March 2015 and had a refund due for 2011 and 2012 that you filed as applied to the next year's taxes, rolling it forward each year until 2013 with remainder for 2014, is this allowed?

My friend did this and the IRS instead refunded 2011 and 2012 and is now charging penalties and interest for 2013 tax due to not enough tax withheld since instead of applying refund as estimated taxes for following year as requested, IRS refunded those years and now say 2013 is paid late.

If this is allowed, what is best way to get their error corrected? If not allowed, what is basis for that?