As described in info page, that behaviour could be expected somehow:
" A successful use of `chmod' clears the set-group-ID bit of a regular
file if the file's group ID does not match the user's effective group
ID or one of the user's supplementary group IDs, unless the user has
appropriate privileges.  Additional restrictions may cause the
set-user-ID and set-group-ID bits of MODE or REF_FILE to be ignored.
This behavior depends on the policy and functionality of the underlying
`chmod' system call.  When in doubt, check the underlying system
behavior."

Anyway, I agree that this behaviour is confusing and user should be
informed, that chmod used different mode than requested. I proposed that
change to upstream at http://lists.gnu.org/archive/html/bug-
coreutils/2008-10/msg00273.html (hopefully is the link correct, message
was not reachable from archive list at the moment of the post).

-- 
chmod not returning right exit code on SGID directory failure
https://bugs.launchpad.net/bugs/187315
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