The primary issue revolves around the selection process for moderation. To become a moderator for a subreddit, you need to have thought of the name of the subreddit. That's it. This nomenclature designation act grants any user absolute power within that domain space, and the ability to grant any other user the exact same powers.
The person who created the "programming" subreddit has no qualifications, no resume by which to judge their aptitude for the moderation job, and no process exists by which to vet newly added moderators.
A moderator can, for any or no reason, decide to activate the "spam filter" on any submitted article, removing it from public voting and view. This is the only tool by which Reddit moderators are given to modify their respective domains, and when used for reasons other than spam, it "teaches" the filter to remove non-spam results. This is the cause of the "broken" spam filter on Reddit - moderator abuse.