This seems like the most appropriate place to post this:
>WARNING TO THOSE PLAYING ORAS
(Or at least alpha sapphire, I haven’t tested this on omega ruby yet)
When you reach the earth’s ‘core’, or where kyogre is, DO NOT use an escape rope!! When you go back to where you follow kyogre to the cave the event where you ride it DOES NOT ACTIVATE!!
You will be stuck forever, and if you saved, you will have to restart your game!
Source (tumblr post)
I just played Alpha Sapphire, and there was a new patch in the Nintendo shop when I booted up my 3DS. I'm not sure if that patch is what fixes this problem, but you should still be aware when facing Kyogre or Groudon.
UPDATE: the version 1.1 patch is for you to connect to the internet, so it isn't something that fixes this.