Underwater Ruins can generate in the sides of underwater ravines. I assume the game is spawning it at the very edge of the ravine floor, causing it to be in the wall. This leaves no opening from the top, which also conceals the chest.
An example of this can be found on the seed -5384628059105572773 at (310,25,-235)
Im sure this is suppose to happen. Its kinda like the bone structure which no one knows of, rarely they are visible and most of the time they are hidden underground.