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.