Google de-indexed Bear Blog and I don't know why

Breaking News: Google de-indexes random sites all of the time and there is often no obvious reason why. They also penalize sites in a way where pages are indexed but so deep-down that no one will ever find them. Again, there is often no obvious reason.

Do you have any resources here? The /r/seo subreddit seems vers superficial coming from an web agency background so its hard to find legit cases versus obvious oversights. Often people make a post describing a legit sounding issue on there just to let it shine through that they are essentially doing seo spam.