It's possible for desert Temples/pyramids to generate completely submerged in the terrain, with absolutely no indication of their existence at the surface.
TO RECREATE:
Seed: 2898554915360970213
Coordinates: x:-3413 z:-334{{{}{}}}
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We're tracking this issue in MC-238647, so this ticket is being resolved and linked as a duplicate.
That ticket has already been resolved as working as intended, which means this is not considered a bug and won't be fixed. Please do not leave a comment on the linked ticket.
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Relates to (duplicates?) MC-238647