If they should have filed a 1040NR instead of a 1040 then they must amend the 1040 to reverse the error and file the correct form.
http://blog.turbotax.intuit.com/2014/04/08/turbotax-and-sprintax-now-make-filing-easier-for-non-resi...
https://ttlc.intuit.com/replies/7276605
