The ability to auto-focus is a great benefit to photographers. Most of the time. But as good as auto-focus can be, there are times when it either fails completely or takes so long that you end up missing more shots than you get.
Camera makers know that their customers want auto-focus. The latest advances are prominently touted in the advertising for each new camera model. Competition between manufacturers is fierce, with us, the auto-focus loving photography community as the direct beneficiaries. During the day, it's convenient to let your camera deal with focus, freeing you up to concentrate on creative composition and other, more "fun" aspects of being a photographer. And as we generally tend to get older as the years go by, it's not unreasonable to conclude at some point that a good camera and lens on auto-focus can lock on focus, faster and sharper, than you or I sometimes can.
Here are some situations where you are better off turning off the auto-focus and handling the job yourself. Manual focus really is better sometimes.
Shooting in Low Light
There are a lot of great images to be made at the edges of light near sunrise and sunset. It's a truly magical time when even the most ordinary of things can be transformed into beautifully photogenic subjects. Light levels and colors change quickly, and you have to react equally quickly if you want to capture such moments with your camera. The problem is, your camera really doesn't want to auto-focus in dim light. It can take an excruciatingly long time to lock on focus without sufficient light, and most cameras will refuse to even try if the light level drops even further.
As the sun goes down and auto-focus begins to struggle, don't fret. If you can find a high-contrast edge the same distance away as your desired subject, focus on it, and then swing your camera around to where you want it to point. If that isn't possible, or you want a way to check your focus, switch your camera to Live View mode to see what you are focusing on more clearly. If your camera doesn't have Live View, just focus the best you can, and then review the resulting image on the camera LCD display back. If you find that you've missed the mark, simply tweak the focus, and try another shot. Zoom in on the LCD image as far as needed to satisfy yourself that things are as they should be.
In order to achieve auto-focus, a lens rotates on its focusing gears forward and back, using feedback from phase detection and other mechanisms built into the camera's electronics. But when shooting close-up and macro shots, even a small turn of the lens can have an enormous visual impact. By the time the camera and lens realize they've achieved focus, its too late, and they end up overshooting the target. To correct the problem, they shift directions and focus back the other way. The same problem with overshooting the mark inevitably repeats itself, over and over again, first one direction and then the reverse. Maddeningly, the lens will hunt and peck, back and forth. The auto-focus algorithms are simply not quick enough or capable enough to find sharp focus without a lot of work, if eventually at all. You're better off switching to manual focus and doing the job yourself. Just rotate the lens slowly enough that you can tell when you are about to achieve focus, and even more importantly, when you reach that point and not go beyond it.
HDR and Other Image Stacking Techniques
High Dynamic Range (HDR) imaging is all the rage these days, and with good reason. Even the best of cameras is only capable of recording a much narrower range of brightness levels than is typically encountered on a sunny day outdoors. By shooting multiple frames over a progressive series of exposures and them selectively combining the results later via software, you can create an image that looks perfectly real, but one that no camera can produce on its own. The eye can see such sights, but people aren't used to seeing photos that do justice to them. As primarily an outdoor landscape photographer, I like HDR images when done well. If you've tried HDR yourself, you've no doubt learned that it's important to keep as much as possible the same other than exposure between successive frames. If anything moves, it can be quite difficult to fix later when combining the shots. And this includes a change in focus. Even if you achieve focus by means of auto-focus, switch the camera to manual focus before shooting so it can't change. For better or worse, that's the focus point you will have to stick with if you want to avoid problems combining things on your computer. If you find yourself wanting to tweak the focus any, do so, and then start the series of shots over again.
Other Tricky Situations
If you've ever tried to photograph an animal in a cage at the zoo before, you know that there are other ways that auto-focus can fail you. Your camera really has no way to know whether you want to photograph that zoo animal or if you want an image of the bars that keep you safe from it. Camera systems generally guess that you want to focus on the nearest point containing anything big enough to lock onto, in this case, the bars of the cage. Not all cameras have such problems with every similar near / far situation, but most will struggle at least sometimes, and probably just when you'd rather yours just do its job. How dare it not focus where and how you want them to. You paid good money for that camera. But its just a tool, and no tool is perfect.
You may also have encountered auto-focus problems on a foggy day or in other low contrast settings. The problem here is the same as in low light situations. In order to detect focus, the camera has to be able to detect some sort of contrast edge to use to test for sharpness. If not pointed toward something with sufficient contrast, there simply isn't enough difference between in and out of focus for the camera to base a decision on.
When auto-focus fails, it can be a frustrating experience. I've met some photographers that simply give up and move on when their auto-focus doesn't cooperate. They're spoiled by the wizardry of modern electronic cameras and they leave theirs set on fully automatic everything. They never learn to take matters into their own hands, either out of necessity or simple desire.
Practice focusing at home before you go out. There's nothing that can make one feel more awkward than to realize they've been turning their lens the wrong way, forcing it ever further out of focus as the golden light of sunrise is rapidly replaced by broad daylight.