I've been experimenting with the /fill and /clone commands to make teleportation based vehicles, like the one in this Reddit thread: http://www.reddit.com/r/Minecraft/comments/1w1re0/warp_ship/
I've noticed that if I use /fill with mode 'replace', the command blocks in a selected region do not change to the selected block. /fill 'destroy' works, but of course that leaves loose blocks all over the place. As you can see in the link, I am not the only person to experience this.

Steps to reproduce:
1. Create a selection that a command block can fill
2. Place another command block in the region
3. Fill the region in 'replace' mode with air
4. Notice that the command block remains