That sounds like a mod loaded after the petshop then changed the land/water level. That used to happen with the Seyda Neen and Haldenshore mods, you could try changing the load order of which mod comes first of mods which are in Seyda Neen. Try a program called 're-order mods' for that if you don't know how. You might try Haldenshore mod too, I think that considers that problem.