Simon in the hangout asked about it because he believed that often, those links are not in Google's index. Simon asked:
In search console when you look at your inbound links, you'll often see a number of pages in there that link to you that are actually in the search index. I don't know why that is and maybe some content is cached or style or whatever. But i think you said in the past, if a page isn't in the search index and even if it's in search console it won’t contribute to any kind of algorithmic penalty filter anything like that. Is still the case?
In which Google's John Mueller responded that those links should be in the Google index. John said:
We should have these pages in our index if they're listed as links in search console.
I mean one aspect that could be happening there is that a page maybe as a no index on it. We know about it, we can crawl it, we can kind of pass PageRank through the links that are there but it's no indexed because there's no index or maybe it's a kind of temporarily hidden with the URL removal tool something like that. Or maybe it was hacked and is hidden from the search results because of that.
But in general if it's listed as a link in search console we should know about that.
John then goes on to ask that if you have examples, send John those examples of links found within the Google Search Console that are not in Google's index via Google+. He will then investigate it.
Here is the video embed:
Forum discussion at Google+.