I noticed that in my survival world, the well in my plains village has path blocks underneath it. I noticed it because the path blocks that I made around it don't get darker at the edges as they normally should. As you can see in the image, once I removed a naturally spawning well block and replaced it with my own, the path block turned into dirt as it should. Perhaps a fix would be to replace the bad path blocks with cobblestone when they are originally generated in the world.