Perhaps you select the wrong focus point? Which camera do you have?
Generally, I use AF for everything except macro, in which case manual focus is the only alternative. By macro I mean macro as defined, magnification 1:1 or more, i.e. not close up. For close up AF is used. I see no reason to focus manually since the AF is faster and more accurate than manual focus. I use center focus point only, aim and recompose if necessary.
