Bonus chest spawned on top of water.
Seed: 5864409455779207650
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This appears to be a duplicate of MC-29613, which hasn't yet been resolved. If you have any additional information to provide regarding this issue, feel free to comment on the parent ticket. If you feel that this issue is affecting you, feel free to vote for the duplicated ticket, to give Mojang a basic idea of how many people are impacted by the problem. Just to further inform you, this will not determine how quickly the bug gets handled or fixed.

Yes, duplicate. Sorry, the search function didn't bring that one up, only another ticket that was marked as solved in 2014.