Just because you have a high end DSLR and the best lenses does not mean it will automatically give you the precise focus required to produce tack sharp images. Assuming camera and subject motion is not a factor then the following will impact on focus accuracy:
The following discussion has been written from a Nikon perspective, but applies equally to Canon, although the focus terminology is slightly different.
The normal focus method employed in single lens reflex camera, which have a mirror that interrupts the light path, is phase detection auto focus. This works by splitting the light and directing the two paths to an AF sensor at the bottom of the camera. By doing this and comparing the result the amount of front or back focus can be calculated, and the lens focus quickly adjusted. For this to work the alignment and distances to the AF sensor must be exactly matched to the alignment and distance to the image sensor. Also, the amount of adjustment focus for the lens must be very accurate. The system may make a second adjustment or it might "hunt" if there is not sufficient contrast to make a determination.
With the advent of digital cameras (DSLRs) a second focus method, live view focusing, became possible - measuring the contrast difference between adjacent pixels on the sensor. This has the advantage of not requiring a secondary light path that must be precisely matched to the sensor. The downside is that contrast detection is much slower than phase detection AF. On the other hand, it is significantly more precise.
When the camera is in single mode the focus locks on the subject and then stops focusing. This works well for stationary subjects. Continuous mode locks on the subject and then keeps sampling and relocking as the camera to subject distance changes, and can even predict the changing distance, which works well for moving subjects. However, using continuous mode to focus on stationary subjects can be problematic as the the focus "micro hunts" making very small focus adjustments - which one is the correct one?
As identified above, the alignment of the lens elements, lens mount, mirror, beam splitter, AF sensors and sensor must be near perfect for phase detection to work well. In the real world this is often not the case, and most DSLRs allow the user to fine tune the focus to adjust for a set amount of back or front focus.
In the following test, using a Nikon D700 and 85mm f/1.4 AF-S lens mounted on a sturdy tripod, a series of trials were shot of the same target to show the impact of focus methods, adjustments and repeatability. The first trial used live view focus, in the second and third trials the lens was unadjusted, and in the final trials the lens focus was fine tuned using the lens align product. The shooting process involved:
From this test we can draw the following conclusions:
So, why do we not notice this all the time? Normally we are shooting at a smaller aperture than f/1.4 with a greater depth of field, so the pinpoint focus is not apparent. Also, we do not have a LV focus image to compare to, and accept it looks okay.