Rarely traversed due to Flotsam and Jetsam learning Pikachu's Thundershock attack, I was wondering if this was either a graphical issue on my end or--
Is it possible to lower the 'height' in which you swim?
When swimming in these areas, the character is lifted up above the ground at quite an extreme height. Although this does give the lake & ocean areas an awesome perception of 3D depth, it actually becomes difficult to see obstacles in the form of placeables or terrain features that block movement, and the tiny transitions & possible quest placeables can easily be missed.
Sounds like a graphical issue on your end. Take a screenshot?