Place the stained glass underwater and Press F5 then Move to the stained glass you placed.
The screenshot is on version 1.7.2 which I ever used. This bug appears in any version including new snapshots. I tested it and it's still there. and kinda hard to take one.
Mojang said I should write this, this is an email from mojang:
Hey there,
Sorry about any delay you're encountering! We try to respond to tickets as quickly as possible in the order they were received.
I'm sorry to hear you're encountering this issue. If you believe that you have found a bug, please report it at; https://bugs.mojang.com/secure/Dashboard.jspa so that a moderator and/or developer can take a look.