what hapened the sink holes?

http://timeline.godzillamovie.com

I imagine (although I don't know) that the sinkholes may be saved for sequels. Or maybe it was a scrapped concept. Maybe they're explained more in the Comic/Novelization/Art Book/DVD Bonus Feature?

Here in this movie, they introduced their 'primorial ecosystem'....which was obviously populated by more creatures and species than just those two MUTOS and Godzilla.

If they all went underground or underwater for radiation, there's no reason more couldn't wake up for various reasons in future films :-)