Yes, manual focusing is more accurate than phase detect AF (except for the combination of very recent Canon camera + lens). Over at LensRentals blog Roger performed AF tests back in July / August 2012. For almost any combination of camera and lens, manual focus can (given enough time) be better than phase detect AF. Read the whole blog series if you want to figure out why some Canon cameras with some Canon lenses perform equally good with phase detect AF as manual focus.

I even have graphs to back me up on this one. First a small excerpt of the blog post to explain the graph.

Then we took eight repeated shots using LiveView and manual focus (represented by red squares), spinning the focus ring between each shot to either infinity or absolute close up. The red squares demonstrate Roger Units (how well Roger can manually focus given all the time in the world on a tripod with a perfect test target.)

Finally we did the same thing but let the camera autofocus in LiveView (represented by green triangles), resulting in contrast-detection autofocus. In theory this should be as accurate as Roger is, perhaps more so.

The graph below shows the results of those shots. For those of you who are not familiar with our Imatest graphs, the numbers reflect the sharpness of the image in Line Pairs / Image Height. The sharpness in the center is shown on the X-axis and average sharpness on the Y. Higher is better and, in this test, better focus equals higher sharpness.

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Now let’s throw away the repeated shot results from above since we’ve made that point, and replace them with standard (phase-detection) autofocus shots. These are taken in exactly the same way as the live view AF shots: take the image, spin the focus ring to one extreme, let the camera refocus, save the image.

It's quite clear from the graph that phase detect AF is not as good as manual, and that the performance varies a lot more. You might be lucky and get good focus with phase detect AF, but far from always.