AF is not magic, the camera will often focus on something other than what the operator wants. However, there are a number of things you can do to improve the results.
First are you using AF.C or AF.S? I always use AF.S, never AF.C, I understand that many of the complaints about Pentax AF are regarding the AF.C mode but I wouldn't know, I never use it for my photography.
Second, the camera has a number of AF 'areas', these are often called 'points' but that can be misleading. Often the AF area is larger than what you intended to focus on, the camera can lock onto anything in that 'area' and be happy. But if it focuses on the nose and you wanted the eye, well you are not happy. In this case manual focus might be your friend. I have a trick that seems to help, not 100% but it does help. I focus on the subject, and after the camera gets a lock, release the lock and re-focus. Maybe I'm just lucky but I find in a good percentage of images this results in a better focus than single focusing. Of course you don't always have time to do that.....
Third, the k-5 has the ability to fine tune the AF on up to 20 different lenses, or if you only use one then it has a global AF adjustment. AF fine tuning needs a precise test, with tripod, carefully aligned target and many repeated trials. If done in a sloppy manner you are just guessing and are just as likely to make things worse than better. But it can make a marked difference if your lens / camera combination is off a bit. As I understand it, both camera and lens are made and adjusted within 'tolerances'. Say this is +/-5 on both. If the camera is +5 and the lens is -5 then the differences cancel and you might have a perfect match but if the camera is +5 and the lens is +5 then you might be +10 out and the miss-focus is noticeable. There are a number of methods to fine tune and a quick search will turn those up.
Fourth, the k-5 has a bad reputation for focus in certain light conditions. In particular low, incandescent light has caused a lot of complaints. If you are shooting often in those conditions then the camera will have problems.
I have never really had focus problems with the k-5. In fact I'm usually confused as to why there are so many complaints about it. I rarely if ever get an image that is not focused properly that I can blame on the camera. I make plenty of errors, but that's my fault not the camera. I realize that I use a particular style of shooting that seems to avoid the issues others have but it works well for me.
Here is my method:
Always use AF.S never AF.C
Always use center point AF only. Focus on the subject using the center point and then (without losing focus lock) re-compose to take the shot.
Don't shoot in poor light or tungsten light. Not always possible of course...
Use AF fine tune on all lenses, I use a Lens Align system on mine but there are other methods.
If all else fails, or I'm trying to shoot an apple in a tree and the camera 'likes' the branch better, well that's why we still have manual focus.
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