Problem with Comment Feeds on Individual Posts

I help run a site that syndicates in content from other WP sites. In some cases we are parsing and displaying content from feeds associated with individual WordPress posts. However, recently a strange bug has emerged. If the incoming site doesn’t have pretty permalinks set, the comment feed from an individual post is wrong — instead of showing a feed of comments it just shows the standard feed of the latest posts on the site. As soon as permalinks are adjusted, this seems to go away.

Is anyone else noticing this behavior?