When the Phantom mob enters out from water, its wings transparency pixels will make the water under its wing invisible from the players perspective. 

On the picture i have added you can see that the phantoms wing has some of its pixels on the wing being transparent, but when this part is over water it makes the water transparent, so you can clearly see what is under the water. For example, in the picture i have provided you can clearly see the grass block down on the ground without water in front of it.

I have tested if I could replicate this bug, and it is very easy to replicate. you just put the phantom in some water, prefely on top and watches it go out or be close to the surface of the water. 
This bug may not be critical, but it can be done to some extent in survival minecraft. You can for example not sleep till a to Phantom spawns, and then go out on the sea. if you are lucky, the phantom will swipe down on you while you are close to the water and you will get a clear view of what lies beneath the ocean. for example, you might see a shipwreak or a guardian temple.