i checked on serebii, it's in a place called "sky rift" in at lv 48, and won't be there until your 2nd visit. you can go to sky rift after you get through "the nightmare" and talk to lapras at the shoreline.
and it looks like you can also get latias, darkrai, and latios in the same dungeon, but you need the stone plate or enigma part, but don't need one of those items to get palkia.
that help?
I heard that you got Palkia at the Spacial Rift.....so now I don't know which one to go to.