The bug 

In Minecraft Java the second layer of the skin can support transparency, some blocks cant be rendere correctly if the player see throught thah layer, 2 blocks have this issue Water and glass, this bug might be hard to reproduce. See videos below

How to reproduce this bug

1- Get a skin that have transparency in the second layer (can be created with paint.net or other photo editor software). 

2- place water or glass 

3- In game use this comand /give @p minecraft:player_head{SkullOwner:PlayerNameHere} to get the skull with the skin

4- put in on a armor stand and try to find the correct position to have the second layer of the skin in front

Expected results

Any block should be able to render properly

Actual results

Water and glass dont render. 

More information

This issue only affects water and glass i tested with leaves and lava, doenst seems to have any problems