This is a specific bug that can really mess you up and waste a lot of water. Specially when you want to make a clean water section and a contaminated water section right next to it.
Excuse me for the terrible quality of the screenshot, I couldn't find a big sized one and the bug is rare so I couldn't make it happen myself. If I'm able to do that again I'll surely post a better one.
When you enclose water with the tiles and you put a tile like it's showed on the screnshot, it will become indestructible, even if a dupe deconstructs it, it will still be there, even if it's reachable aswell. If you did it and you were able to deconstruct it, try deconstructing the floor and make another floor below it but leave a tile.