When I loaded this world in the new snapshot, I loaded with Generate Structures on in Superflat, there was a cross-over with Normal generation and Superflat, this is a must fix bug!
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Duplicate of MC-315 - If you have not, please use the search function in the future, to see if your bug has already been submitted. If you could not find the original report, please comment with the keywords you searched for.

Yeah, did not know, because right when I saw this on MC, I wanted to post it as bug, so.