What exactly are you scanning? If you’re scanning red book audio CDs (AKA “Compact Disc Digital Audio”, or “CDDA”), that could be due to the lack of error correction in the standard. Basically, drives have to take a guess as to whether the data is being read correctly or not. Also, there may be instances where the drive starts and stops (such as when the computer lags), which is a problem because it’s very hard for the drive to guess where to resume reading the data from. On top of which some drives suffer from alignment problems and/or firmware bugs. (See this well-written article for more info.)
Of course, these issues only really affect red book audio disks. If you’re burning some other disc, you’re probably using a more error-resiliant file system, such as ISO 9660 or UDF. These file systems have error corrections and sector markings that prevent these issues.
Have you tried using different drives? Maybe the drive you’re using has firmware bugs, or maybe your drive is malfunctioning.
Also, are you using a laptop with a built-in drive? Or are you using an external drive (on any kind of computer, not just laptops)? If either of the above are true, maybe the drive is being physically moved too much (that is, moved from one location to another)? Make sure your drive/laptop is set on a stable surface (such as a desk), and leave it there until the scan is complete. Obviously this doesn’t really apply to desktop drives, unless you’re physically shaking the whole computer for some reason.