when something goes above the height limit and your looking at it through a cloud it becomes invisible above the height limit
to re-create
1. reach a few blocks from the height limit
2. make a big jungle tree on that layer, going past the height limit
3. go right below the cloud layer and observe above the height limit it becomes invisible.
This picture shows a server with a height limit that is at the cloud level,
I'm looking through a cloud and just above it he height limit is reached and the blocks no longer display.
(This May affect other versions of Minecraft including most of them before 1.7.5 for sure)
Linked issues
duplicates 1
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Duplicate of MC-997
This is not a bug. Clouds will obstruct your view and you can't see any blocks above the height limit because there aren't any blocks above the height limit - that's why it's called a limit.