It's a bug, of course. Google's routine that estimates the total number of pages on a site: query can seem to have more trouble with smaller website. On a 5,000 page site or a 500,000 page site you wouldn't even miss 50 pages!
It's also good to remember that the site: operator is a reporting function and not the core of Google's search product. As such, precision in those numbers is definitely NOT a top priority for Google.
[edited by: tedster at 4:29 am (utc) on Aug. 8, 2008]