Blocks can disappear or be "duplicated" when they travel through different chunks.
Here, another piston head is created. But if it's the redstone block that moves between 2 chunks, it will sometimes disappear. These are not ghost blocks.
To reproduce, build that kind of clock, and unload and reload the chunks. You may get this. I got it several times at the same spot.
A possible important thing to say : these 2 chunks were in my spawn chunks before I changed them by /setworldspawn somewhere else. But they weren't the edges of spawn chunks, or lazy chunks. (This is happening after the change)
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Was messing with that bug in 1.9.3-pre2 trying to recreate it. Unloading and reloading chunks and redstone don't seem to work quite well together : https://i.gyazo.com/d55644525b39fd565a0a979579d41d83.gif !
The gif can't show that in the left hopper the item appears really fast, and in the right one, it stays a little longer.
And it's not a visual glitch : the right piston couldn't push the redstone block whereas it was powered, and the left one wasn't.