The "problem" with the 50/1.2 is focus shift. Focus shift occurs because the lens focuses wide open, but when the lens stops down for exposure, the point of sharpest focus shifts rearward. This is inherent in the design of the lens. My 50/1.2 exhibits focus shift at apertures f/2 through f/5.6 combined with short subject distances. Wider than f/2 there is no appreciable focus shift. Narrower than f/5.6 the depth of field expands sufficiently to obscure the focus shift. At subject distances greater than a few feet, the focus shift is not detectable even with testing. In fact, I can only detect focus shift at the problem apertures and range when I test for it. In "real world" shooting, I have never noticed focus shift. Rather, many other factors not related to the lens itself affect the quality of focus, such as subject or camera movement, poor light, high contrast backgrounds, AF point size, etc.
I also use the 85/1.2 Mark II. It does not exhibit focus shift, but it also does not focus as closely as the 50/1.2. If I were to never focus my 50/1.2 closer than the 85/1.2 minimum focusing distance, my 50/1.2 also may not exhibit focus shift.
Many fast (wide aperture) primes exhibit focus shift, according to what I have read. I am not a lens designer, but my understanding is that focus shift is a design trade-off to gain other lens qualities. While the 50/1.2 is berated for suffering from focus shift, the most commonly recommended alternative to the 50/1.2, the Sigma 50/1.4, also exhibits focus shift almost identical to that of the 50/1.2, accrding to tests available for a fee at the diglloyd site.
Some users of the 50/1.2 claim you can work around the focus shift by using only peripheral AF points. This may be true, but when I tested that workaround, it had no effect on my 50/1.2's focus shift. Therefore, I use no AF workarounds -- or any workaround at all -- with my 50/1.2, and focus shift has never been discernible in my real-world shooting.
Manual focus does not prevent focus shift, but presumably one could manually focus slightly in front of the intended point of focus to counter the focus shift. I cannot manually focus that accurately to even attempt such a feat. One could also sway backwards slightly after locking focus, or focus on the tip of a nose instead of an eye, when shooting in the danger zone (f/2-f/5.6, close focus). Again, I do none of this.
Sean Reid on the pay portion of his site has a fine review of fast 50mm lenses for Canon, including the 50/1.2, the Canon 50/1.4, the Sigma 50/1.4, and the Zeiss ZE 50/1.4. His conclusion is that the 50/1.2 is the superior lens. I haven't used any of those other lenses, but I can say that the 50/1.2 is my favorite lens on my 1DsII.