The chrono hand should reset to 12 and this should be fixed under warranty.
The Speedmaster is not a hacking movement - it's not a "quirk", it simply does not have that functionality. You should be able to get the second hand to pause by keeping backward pressure on the hands when setting, but honestly it's not worth the trouble - it's not chronometer rated either, it'll be out by a few seconds daily anyway.
Get the chrono hand fixed and enjoy wearing it.