Prior to UFC 98, I noted a tendency in Rashad Evans to "walk backwards." The basic tenet of boxing footwork is to lead with the leg nearest the direction you want to travel. An orthodox fighter will lead with his left leg when he wants to move forward or to the left, and his right leg when he wants to move backward or to the right. Rashad would often, for instance, lead with his right foot when stepping to his left.
Improper footwork might seem like a small problem, but it can have huge consequences. Sound footwork maintains the integrity of a proper stance (feet shoulder-width apart, bent at the knees, etc.). When you compromise that integrity, you run the risk of losing balance; losing efficiency in movement; an inability to capitalize on mistakes; and susceptibility to takedowns, leg kicks, and other offensive attacks.
Rashad's footwork flaws (he also had a tendency to leave his feet when jumping in with a punch) led to him showing us his stanky leg against Lyoto Machida. I've seen improvement since that fight, though I still see some issues with his lateral movement.
The first instance of Jones' footwork comes early in round two at UFC 126:
Now, that's a mistake that he can get away with given the distance between him and Bader, but this isn't an isolated example of Jones' footwork either. The problem is obvious, though: Jones makes two obvious steps forward while leading with his back foot. Notice Jones' stance after he plants his back foot:
Here's another look later in the round:
Jones again leads with his back foot. I'm also not fond of the length in Jones' stride, either. It should be obvious that if footwork should first work toward maintaining a proper stance that it would benefit a fighter to use short, quick steps instead of long, broad ones.
And while there's a ton of caveats to the point, I'd like to note that Stephan Bonnar outlanded Jones in total strikes at UFC 94 (74 to 70).
As for his ground work, Joe Rogan made a big stink about Jones' arm placement while in Brandon Vera's guard:
Look at all the space Jones is giving to Vera's hips! It looks like Vera's focused on controlling Jones' posture with his left hand. I also want to assume that Jones is scary strong because he was able to get away with this a few times during the fight. The issue here, though, is that he's putting his arm in a very precarious position. Vera can grab the hand with his cross arm and pull across, knock the arm across with the same-side hand, or use a two-one-one grip to pull across. With the arm across the center line, Vera would be in great position for an armbar or to take the back (among other things).