After pressing M-s-a, I get the message:
M-s-å is undefined
Expected: M-s-a (being defined or undefined)

Tested running Emacs as a Carbon app on OS X:
open -W -n -a /Applications/Emacs.app --args -Q

After pressing C-s-a, I get the message:
<C-s-268632065> is undefined
Expected: C-s-a (being defined or undefined)

Seems to happen for all keys, not just a.  For C-s-<letter>, the
character produced is 0x1002ffa0 + <letter> instead of <letter>; for
M-s-<letter> the character produced is whatever OS X maps to
Option+<letter>.  This happens only if Super is pressed as well.  More
discussion at
http://lists.gnu.org/archive/html/help-gnu-emacs/2015-02/msg00503.html.