What lens (or rather lenses) are you using? I'm really puzzled. Do you see the focusing point in the viewfinder or have you disabled it? Maybe you have set an autofocus point that is way out of where you want to focus on. What kind of autofocus mode do you use? AI Servo or One Shot? Because if you use AI Servo and you recompose the shot, you lose focus. When setting your autofocus point to automatic and firing off shots in One Shot mode, you shouldn't have any problems whatsoever.