I expected the command blocks to follow their commands, however, after quitting and saving and then replaying a certain command block world I had, I realized that the command blocks were not following what they said was written in them. Originally I thought it was a certain NBT tag that wasn't compatible with /testfor, but then other things that were working stopped working, and then once I rewrote them again, they worked again.

In some cases I got 'this command does not exist' or 'missing bracket'.
The errors always seemed to have something to do with the characters on the ends of the strings not being loaded. <-INCORRECT: I just got an error in which an NBT tag in the middle of other brackets that are working is not working.

Update: (In response to Anon Ymus)

I was using the /summon and /testfor commands. I was in the process of trying to figure out how to test for an object being in someone's inventory, starting out by listing the

 {Equipment:[{id:<Item>}]} 

NBT Tag on Zombies. I managed to get the

 /summon Zombie ~2 ~ ~ {CustomName:"George",CustomNameVisible:1,Equipment:[{id:minecraft:iron_sword},{id:minecraft:iron_boots}]} 

command to work as well as

 /testfor @e[type=Zombie] {CustomName:"George"} 

. However, later in my testing when I was working on trying to get

 /testfor @e[type=Zombie] {Equipment:[{id:minecraft:iron_sword}]} 

to work, Suddenly my Summon command block was not spawning the zombie. This was the first time I had pressed the button to activate the command block since I had reloaded the game, which I had already done several times, and now it wasn't working. All the text looked fine. I remember it first complaining about brackets on the NBT tags, so I retyped the }]} at the end and than that worked for the equipment, but then the name wasn't working (it said Zombie above it's head, not George), so I retyped the name just as it was already, and then that worked.
Now I'm not sure if Equipment tag works the way I wanted it to or if it's just this same bug that must have loaded the command for the block from the text incorrectly or what. I've been unloading and reloading the world for a little bit and haven't been able to replicate it yet, so it might just be a one time thing.