This happened when we upgraded our server from 1.8.4 to 1.8.6.
Every two-high flower in our world switched to a ghost peony, no drops of the previous item or anything. If you left or right click it, it will go away on your screen only to come back when you reload the area. If another player is watching you, they won't even see the peony disappear when you punch or right click it. The only way to rid ourselves of it was to put sand over it until the sand covered the peony completely. The sand falls right through the floating peony onto the ground, and a second sandblock will land right in the peony covering the graphical glitch up. Then when you break the blocks and reload the area, it will be destroyed for good. This doesn't drop any items, so all the two high flowers in our world are currently dead.
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Really weird.
kumasasa
Does this affect by world generator placed plants or manually placed or both ?
Can you provide a seed and coordinates of an area of world generator placed plants ?
In what version of Minecraft was that world created ?
marcono1234
Relates to MC-62140
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Dupe of MC-62093