Even though autofocus, which is a function that automatically adjusts the lens of your camera to focus on the subject you're photographing, works very well most of the time, there are a few shooting scenarios where you may find that auto focus struggles to lock focus or focuses on the wrong thing and if this happens, you'll need to switch it off and turn to manual. Nikkor lenses have smooth, grippy focus rings, to help you get focus really accurate.
Not Enough Light
When shooting in situations when there's not much light around your lens, when on auto focus, can end up searching for something to lock its focus on. Some cameras do have a focus lamp but it doesn't always help, particularly when it's late at night and there's no light at all. Shining a torch in the spot you want your camera to focus can sometimes help but for shots of light trails, star trails and light painting, for example, you're better off switching to manual so you can ensure what needs to be in focus is.
Lack Of Contrast
If your subject has similar textures, colours and tones to what's behind it or if you're just taking a photo of something, such as a wall, that's plain and doesn't have much contrast your lens can struggle to focus when in AF. By switching to manual you can tell the lens what you want to focus on so the white flower in front of a white background will be the point of focus in your shot.
Having a camera with a quick auto focus system will help you capture fast moving objects but sometimes, even with great panning skills and continuous focus, it can be tricky to capture the right shot.
To combat this, turn off your AF and switch to manual, pre-focussing on a spot you know the car, person or whatever you're photographing will pass through. You need to switch to manual as auto can decide to change its focus when you hit the shutter and you can end up with an out of focus shot. Remember to lock your focus once you have the right spot focused on and hit the shutter button just before your subject moves into frame.
When you're shooting HDR work you need to take a series of shots you then merge together in your chosen software. For this to be possible you need to make sure the camera's position and focussing point doesn't move. If it does, the shots won't line up correctly when you combine them. Using a tripod, focussing manually then locking the focus will mean nothing moves so your shots should line up.
When Something Is Blocking Your Subject
Animals at zoos, for example, tend to be in cages that are surrounded by a fine wire mesh that often rises above eye level. This means you often have to take photos with the cage in front of you. If you don't adjust the camera's settings and position you will have poor photos which can seem like the cage was your main point of interest thanks to auto focus picking that out instead of the animal.
To compensate, if your camera has manual exposure control, adjust the aperture so it's at a wider setting, this will reduce depth-of-field (front to back sharpness) and throw the fence out of focus. Hopefully the fence will be so blurred it won't be seen in the photo. Try switching off AF too so you can focus the lens on the animal and not the fence. It will also help if you move as close as possible to the fence then position the camera so the lens is pointing through one of the gaps or, when the fence has small gaps, make sure that the face of the animal you're photographing is in a gap.
Multiple Exposure Portraits
As with HDR, the process of shooting these types of portraits involves you taking several shots that you'll need to merge together in one frame. If you're working with plain backgrounds auto focus and white balance shouldn't have too much of a problem but if you're shooting on a busier background you may need to focus and set the white balance manually to ensure it's the same for each shot you take. Make sure you use a tripod so the camera's position doesn't change.
When you're working with such as small depth of field your lens can struggle to focus and end up searching without finding something to focus on. Switch to manual and you can make small adjustments until you're happy that your macro subject is sharp.
When you're shooting landscapes you want everything from front to back to be sharp and this can involve finding the hyperfocal distance. When you have, you don't want to be using AF to find it refocuses the shot as you press the shutter. As a result, try focussing manually so the focus doesn't change unless you knock the lens barrel of course.
Shooting Through Glass
Places where you have to shoot through glass – on a plane, at a museum where there's exhibits protected by glass containers, or the zoo – fingermarks, scratches and reflections can confuse the auto focus function into thinking that these are what you want it to focus on and not what's on the otherside of the glass. Switching to manual focus can help ensure your subject is sharp but if the glass is so badly scratched that anything you take will be slightly fuzzy.
Fog Covered Scenes
As ePz member MollyOcean suggested, it's sometimes worth switching to manual when shooting in foggy conditions as the camera may try and focus on the curtain of fog in front of you rather than the scene you want to actually capture. More fog and mist photography tips can be found in this tutorial: Tips On Capturing Landscapes In Fog And Mist.