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Only Poliwag and Poliwhirl learn Hydro Pump, at level 51. Usually final forms of Poke's which evolve with a stone learn different moves than their previous forms.
Found another bug to report. After beating Elite Four for the third time, Bad Egg replaces 1 of my Pokemons in PC box 4. It wouldn't be that bad but it replaces Raikou, checked 3 times if it happens, and every time result is the same.
Try running around the area, or take a walk around the whole region, I'm not sure. I had the same problem and after like 2 hours of walking around, battling, catching, exploring caves and such they finally appeared. There's also a professor after you leave Ilex Forest on the way to Goldenrod...