PUNCHED HOLE
Punched holes on CDs or records are done when an item was either deleted from
inventory by the record company, or issued as a demo copy. What this meant
is that the artist was not paid for this item as it was not considered sold or
saleable. These holes are purely cosmetic and don't affect the CD or
record in any way.
Below are two samples from the back of CD inserts.

Click on image for a larger view.
The following are two samples from
records.
In the case of a record, the hole is always in a corner and goes through the
front and back of the cover.

Click on image for a larger view.