This was caused by some faulty code in the "Rebuild Article List" tool. Apparently some threads were being saved with the wrong Namespace ID whenever this tool was used.
This would result in a bad article request. Normally, when this occurs, the user should be redirected to the same thread on showthread.php. However, in this case .PHP-less URLs are enabled, and they are actually redirected to what appears to be an article called "showthread.php."
Fixed the code in admincp/vaultwiki.php and ran the URL generator on bad requests to avoid the second part.