When stained glass panes are in front of (flowing?) water, transparent vertical lines sometimes appear, hiding both the pane and water - showing the block behind them as if nothing were in the way. I found this usually happens if you look away from them and then look back, and that reloading chunks/textures using f3+a or f3+t temporarily fixes the issue.

This could be a duplicate of MC-131203, however I believe that only applies to source blocks and is a visually different bug, as far as I can see.

This happens with both fast and fancy settings.

Smooth lighting does not seem to affect it's appearance, neither visually or in rate.