Its in dotted hole not lost cave, in dotted hole fall down the first hole then you will see four holes fall in them in this order: up, left, right, down then take the sapphire.
In ruby u can't find Kyogre only Groundon in sapphire u find Kyogre in Lost Cave on the wild see
In granite cave.
You have to find him in a cave, id say the elite four cave
In sootopolis.
in the littleroot cave
get the HM dive and dive down and you'll find a cave entrance
In Dewford at the cave, Not hard to find.
Go inside shoal cave.
in the cave where aaron are found
you will find him underwater in a cave
You find Kyogre in The Cave of Origin in Sootopolis city
You can find it in the shoal cave near mossdeep where the ice part of it is.