Answer written for the following question that was closed by the OP as a duplicate of this question. There are some other issues in play that answer that other question beyond the issues identified in this question:
Why is fine focus adjustment sometimes necessary on DSLRs? [duplicate]
Many DSLRs have a "fine focus adjustment" option, stored in the camera per lens.
Why is it that some lenses need this?
Why do some lenses not project a focused image onto the sensor when the camera body has adjusted it to a point where it believes focus is correct?
I assume this is a side effect of NOT using the sensor itself to confirm focus, using the phase detection array instead...
It's a side effect of a LOT of things that all conspire to make minor focusing issues more noticeable than they once were.
- For most PDAF systems, neither the PDAF sensor nor the imaging sensor confirm focus. Rather, the PDAF measures the amount and direction of defocus and instructs the lens to move by that amount. If there is any confirmation, it is usually based on a position sensor in the lens confirming that the lens physically moved the instructed amount. This confirmation is often done while the mirror is swinging up and the PDAF system is already 'blind'. With PDAF there is no confirmation that the desired object is in focus but only confirmation that the lens moved as instructed. Only the newest cameras and lenses are capable of even that type of confirmation.
- Digital sensors are a lot flatter than most film was at the time it was exposed. Errors in focusing that would have been hidden by the imprecise shape of the film (and, in the case of color film, the varying depth of the three separate dye layers) are no longer hidden by much flatter digital sensors.
- Digital sensors continue to increase in resolution. Errors that were once within the tolerances of larger pixels are now large enough to be detected by smaller pixels. If a blur circle is smaller than the sensor's pixels it is no more blurry than a theoretically perfect point of light. If that same sized blur circle is larger than the much smaller pixels in another camera, it is detectable as blur compared to a smaller blur circle or point of light that is still smaller than the smaller pixels of the second camera.
- Lenses available on the consumer market continue to increase in resolution. Focusing errors that were masked by blurrier lenses are no longer masked by much sharper lenses. If the focus error created blur smaller than the maximum resolution capability of the lens, it wouldn't be noticeable. If the same amount of blur is larger than the maximum resolution capability of a different lens, it can be detected. In the past some of the sharpest consumer lenses were manual focus only (many of them still are). Thus variation in PDAF systems have no effect on images taken using manual focus only lenses.
- The current resolution of camera sensors and lenses exceeds the tolerances to which we can manufacture them at reasonable cost. Not only are tolerances as small as 50 microns too large to go undetected with regard to the 'squareness of the camera's lens mounting flange to the camera's sensor, but there are also tolerances that are larger than the minimal variations we can see the effect of with regard to PDAF array positioning, lens focus element movements, etc.
Roger Cicala, chief lens guru at lensrentals.com, has written series of blog entries regarding both manufacturing tolerances and Autofocus Reality.
Regarding manufacturing tolerances, please see:
This lens is soft and other myths
This lens is soft and other facts
Optical Quality Assurance
For why sensor resolution matters with regard to how well we can see where a lens is less than perfect (and all real lenses are less than perfect, not just in their implementation but also in their design if they are intended to image more than a single wavelength of light), please see:
Why We’re Going to Start Testing Cinema Lenses. And Why We Haven’t Before.
For further reading on AF systems, Roger Cicala's Autofocus Reality series is very insightful: Part 1, Part 2, Part 3A, Part 3B, and Part 4.
And: How Auto Focus (Often) Works