Sometimes when looking through stained glass, the water source rendered incorrectly.
Before 13w42a the water source occasionally show a bright blue color like viewing from outside (the third picture). In 13w42a and later versions the water source sometimes disappear (the first picture).

Also confirmed in creative mode.

How to reproduce:

1. Select world seed: 8707954756559826592
2.Go to x=-105, y=71, z=1 and build two-block-high stained glass panes there (like the fifth picture)
3.Stand in front of the glass pane and face west (like the fourth picture). You can see the water at the northwest direction disappears.

I have no idea what exactly caused this glitch yet.