When I surfed with kyogre, instead of a dark shape, it actually looked like the top of kyogre. Does this happen with any other Pokemon?
Yes! Infact this happens with 2 other Pokemon. It works with dive too!
Kyogre - what you have - can move slightly faster than regular Pokemon and you can fish on it too. Also, it takes up a much larger area, so you can't get into tight spaces (if there's any)
All other Pokemon are miscellaneous - can't recognize
All information here : http://www.serebii.net/omegarubyalphasapphire/surf.shtml
Hope I helped! Please like if helpful :)