When cloning or filling a large area with blocks, some wither don't get replaced (when filling) or don't get placed (when cloning). I can't reproduce it consstently, but have encountered it many times.

In particular I have encoutered the following (sadly I didn't get screenshots):

1.  Cloning a slice of 30x15x2 blocks repeatedly, some blocks (the furthes away from the player) sometimes failed to be placed without eny arreor mesasage. These were not pistons or blocks moved by pistons, but were actie components (observers, repeters, trapdoors) that might have been powered when cloning. I have noticed that when cloning a movin or extended piston either it or the blocm it's movin can fail to clone or drop as an item when cloned. I used 

   clone 0 5 0 30 20 1 0 5 ~

   moving the player two blocks each time to place the two wide slice many times. As shown here, I used the default values for clone (no replace, no force, and so on).

2. Filling an 8x15x11 area with white stained glass. Before filling, the area had no airblock and was full of observers, pistons, string (tripwire), trapdoors, solid blocks (white concrete) and more white stained glass. After running the command, some string had not been replaced by the glass, leaveing some lines of string inside the big cube. The command, which did not give an error message, was something along the lines of 

   fill ~ ~ ~ ~7 ~14 ~10 minecraft:white_stained_glass