Issue:

1) Water Texture not displaying through Stained Glass or tinted Glass

How To Replicate:

1) Place Stained or Tinted Glass and look at the Ocean the top Glass block will delete the Water Texture. (Tested on Different colours of glass)

Temp Fixes (If you can call it that)

1) If you Jump the water texture Comes back until you are stood on the ground again,

I have attached Screen Grabs of this, also happens in Creative and Survival and Hardcore.