I haven't found their brief to the Supreme Court, but if they raise the same arguments that the raised in their earlier amicus brief to CAFC [1] where they urged CAFC to take the appeal from the district court, their objection is not to the
outcome of the case (Google not infringing) but rather to
how the district court got there.
Briefly, they believe that the district court went too far in declaring that APIs are not subject to copyright in general. Instead, they believe that APIs are subject to copyright under existing statutes and precedent, but that there are various doctrines (fair use, merger, and others) that can allow copying for interoperability.
[1] http://cdn.arstechnica.net/wp-content/uploads/2013/02/MSFT-O...