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.
Please could you provide some additional screenshots of this issue occurring whilst the F3 Debug screen is enabled. This is believed to be an issue with your resource pack, so please let me know if you are using one.