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Late to the game, but Deep Crawl is great for large sites, where Screaming Frogs, even with increased memory allocation, tend to force close the application from such large crawls.

Console tends to show historial data, so those odd sites might not exist anymore. Another thing to do is to see if the actual URL is placed in the HTML, and just hidden by CSS of some kind, whether intentional or not. Focus time and effort reclaiming the real links and doing white-hat work, Penguin runs in real time now.

I would not so much focus on those links, since Penguin runs in real-time now, recrediting those links rather than "punishing" your site. I would focus that time finding unlinked mentions, and reclaiming the real links. Redirecting your highly linked content is good for preserving link equity no matter those odd links.

If you are allowing search engines to index all the pages, then the overall link equity is flowing through.

I would not so much focus on those links, since Penguin runs in real-time now, recrediting those links rather than "punishing" your site. I would focus that time finding unlinked mentions, and reclaiming the real links. Redirecting your highly linked content is good for preserving link equity no matter those odd links.