EDIT: On further testing it seems to only happen with slime blocks. More interestingly, it actually turned them into signs. Not sure why.
If the /clone command is used on a piston that is in mid extension (or mid retraction), it bugs out the block it's pushing/pulling and itself. Powering it and block updates do not fix it, nor does relogging. The only fix is breaking and replacing both the piston and the block it pushed. Have not yet tested what happens when more than 1 block is being pushed.
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Confirmed for 1.10.2 I was cloning something with pistons on my server and I kept getting it wrong, so I decided to build it by hand, but then in one of the blocks there wasn't air although every player hadn't saw there anything, and right clicking, F3+a, the looking at part in the debug menu, relogging didn't help, only /setblock ~ ~ ~ air. I know I could use /testforblock to check what block it was and give more information, sorry.
@Galaxy_2Alex it is for you.
I suggest resolving this as duplicate of MC-129017.
Thank you for your report!
We're resolving and linking this ticket forward as a duplicate of MC-129017, as that ticket contains more detailed information and/or has already been triaged by Mojang.
If you would like to add a vote and any extra information to the main ticket it would be appreciated.
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Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases. If this has been done, we can reopen the issue.
Keep in mind that the "Resolved"-Status on this ticket just means "Answered", and that we are waiting for further information on whether this issue still exists or not. We will reopen it as soon as the requested information has been delivered.