I think this might fit better on the suggestion/feedback site rather than the bug tracker?
You'll probably need to elaborate more. Is it on a server, in single player, if any events you did led to this, etc.
What are you using to mine these ores? Wood, stone, and gold picks can't mine redstone or diamond ore. (By can't mine I mean the ore won't drop anything.)
I don't think this is a bug, as everything is working as intended. The well is structure is being spawned in correctly, (by that I mean no blocks are missing or added) and villagers walking into water can happen, and I don't believe that is unintended. Besides. this problem can be easily fixed by mining some cobblestone to allow the villagers out.
Still hasn't been fixed. Really annoying. Used the fn key for changing perspective.
This is funny enough that I kinda want it to stay in. If it causes negative gameplay effects though then obviously remove it.