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.