The CD encoding technology is a transition technology. If you look at post #362, transition between pit to/from land defines a 1. Using EFM (eight to fourteen modulation) the 8-bit words of PCM are translated to EFM using a precise look-up table so that there are no consecutive 1's. If a pit or land is too long or short, then the code returned is wrong. Some of this can be corrected with Reed Solomon code (but this is HARD). Even with error-recovery technology, you can still return a "correct" result. But the "correct" result can be different from what was intended. That is why the same technology used for Music CDs is not used for data storage. (This is the basis behind EAC and dbPowerAmp by the way - checking against the CRC (cyclic redundancy check) allows the software to determine if the recovered track is the same as other tracks recovered by other people who ripped the CD.)
Error can come about because the physical implementation of the CD is imperfect. When looked at in the data form, the transition between pit and land is very clear. Unfortunately, in the physical media, it may not be clear because the edges of the pits and lands are fuzzy. In a burned CDR, scarring of the edges can occur. In pressed CDs, the edges are not precisely sharp. Depending on the reader, the pits and lands could be read longer or shorter than they are supposed to be.
Moreover, while an off-center LP is easily detected because we can see the tonearm swaying, we cannot see the servo of the laser head frantically trying to keep the spiral of pits and lands on the CD in focus. This results in electrical activity from driving the servo-motor interfering with the DAC, and the laser reading interfering with the accuracy. This is one big unseen problem of CDs that cannot be addressed with damping rings (which may address up/down vibration of the physical disc), green pens, etc. None of this can be fixed in real-time, which is why high-end CD-transports have increasingly been buffering readers. But because they are not connect to the Internet, cannot check the CRC and then go back and re-read the track.
The technology covered in the Black CD White Paper tries to overcome some of this, firstly with better CDR blanks, lowering the vibration to the CD burner, and finally with the Yamaha-patented Audio Master Mode which sacrifices some recording-time for better land/pit transitions. The improvement we heard when we found a CD-pressing plant willing precisely center the CD blank was probably one of the biggest advantages First Impression Music had making better sounding CDs.