The /fill command glitches and will not fill in an entire area properly at times if used on a large area. Example, if done over a 100x100x5 area, filling that area with air creates glitches such as the area either simply not filling, or leftover textures of the no-longer-existent blocks, aka "ghost blocks". A similar problem is that at times, filling small areas or using /setblock DOES place those blocks, but they are invisible until a new block is placed or broken near by, revealing those blocks. Note that the outline of these invisible blocks is still visible, but the block itself is not until there is a new block placed.
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Cleaning up old tickets: This ticket has not been updated recently (~1 year+) so is being closed as Cannot Reproduce. If you feel this is still a valid issue then please comment, or create a new ticket following the Issue Guidelines.
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I'm noticing a similar problem. I have an opening/closing garage door on my house via command blocks that fill the rows of the door with air or blocks in sequence and "move" them from the doorway to overhead and vice-versa. When I push the button though, visually, the blocks don't "move" or disappear (get filled with air), but I can walk through the blocks and from inside them see through the ground in places. The invisible outline of the blocks highlight overhead when I move the cursor there, and they block my way like they're solid. The button also didn't visually depress, but did audibly click. The doors also open and close audibly with the same invisible outline situation. These animations were all laggy in 1.4 and 1.4.1, but now in 1.4.2 they don't seem to work at all. This all applies to an old world that was converted when infinite worlds became available. I'm playing on a Samsung Galaxy S7 edge with the Amazon version.