Here I found a graphical glitch when placing TnT over water, here is the video, (You have to build the walls around the TnT like it is in the video) https://www.youtube.com/watch?v=MAtL82XnUgQ
Environment
OS Windows 8.1
CPU Intel core i7 4790 @ 3.6GHZ
GPU NVIDIA GTX 780
Java Info
Version - 1.7.0_60
64 Bit version
As far as I can tell, this issue occurs with practically any block on top (glass was the only exception I found), and either lava or water on the bottom.