If you enter the locate command and teleport to the given coords you will usually end up in blocks
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you know that the surface blocks of terrain doesn't have same "y" parameter?
So if you locate a stronghold (ex. coordinates: 1200 y 900) and it was under a mountain, when you use "/tp 1200 ~ 900", you may teleport inside the blocks of mountain
violine1101
See MC-143512. This is not a bug.