After the time where you battle Kyogre/Groudon in the Cave Of Origins, you cannot battle them again. I dont know if it's different in Emerald, but thats how it is in Sapphire and Ruby

I don't know about how to fix your problem, but to nullify misunderstandings for others wandering upon this page, you don't fight either Groudon or Kyogre at the cave of Origin in Emerald, both Groudon and Kyogre are awoken and start a terrible battle in Sootopolis bay. You cannot fight them both, so instead you go to awaken Raquaza, the ancient sky pokemon, who in turn calms the pokemon of the land and the sea, and sends them away. After defeating the elite four, you are supposed to be able to go to the weather institute and a scientest on the second floor tells you that there's strange weather on such and such route. Go there and find either Kyogre or Groudon, and then go back to the institute to get the location of the second. So you can catch both, just have to wait until you defeat the elite four. So I do not know why he had a problem, unless he used cheat codes to get his badges and didn't activate all the parts of the main quest as he progressed through the game. The only thing I can think that it MIGHT be, and this may not be it, it there's a cut scene on Mt Pyre where Archie and Maxie return the two orbs, maybe you haven't witnessed that cut scene? I do not know if that's required though. Also, hear the old mans new version of the history of the three ancient pokemon if you haven't, just to be sure.

The Kyogre/Groudon battle is before you beat the Elite 4. if you killed the legendary, i suggest you restart the game. If you go to catch them buy ALOT of Ultra Balls. Save your Master Ball for Raquaza or Latios/Latias Happy Gaming! ~Eclipse

well if he tells you that there are abnormal weather conditions that means groudon and kyogre are on the route that the guy says were the abnormal weather conditions are.