Steps to reproduce:
1- Place a bunch of shulker boxes and wait for the autosave
2- Right after the autosave, mine them, pick them up, and then crash the server
3- When you start it again, they will remain placed and also be in the player's inventory
This probably also happens in singleplayer but I haven't tested it.
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We're tracking this issue in MC-25488, so this ticket is being resolved and linked as a duplicate.
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