Tile entities such and chests and signs sometimes remain after a fill or clone command is performed that should be overwriting them.
I've noticed it happens a lot more after teleporting in and out of the area, also if there are either a lot of entities or if you're doing multiple fills/clones on the same area.
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I cannot as I don't have one I can release to the public. However I have made a private bug report which has it attached.
Searge and Jig, I can confirm this bug exists, but it's been reported at MC-64161
Reopened as of MC-101707
Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w43a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.
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If this still happens in snapshots/versions after 14w34 please reopen this. It should be fixed, but we'd like to have more feedback on this.