Google has often said that there is only a selection of URLs that will show as links when viewing the report in Google Search Console.  But John Mueller made an interesting comment about the differences in links between small and large sites, and in the links they show.

We don’t have any strict guidelines on what’s shown there and what’s not.  It’s essentially a sample of the links.  So for smaller sites, it’s probably more closer to all of the links,  for larger sites it is definitely a sample where we try to show the ones that are more relevant.

It doesn’t take things out that are nofollow, it doesn’t take things out that are in the disavow file.  So it’s more a matter of we know all of these links exist for your site, and here is what we think is a relevant sample for yours.

He was asked for more clarification about what would qualify as a “smaller site” but he didn’t give any specifics.

I don’t know where we would draw the line there.  But it’s something where we have a limited storage available for these links within Search Console, so at some point they get cut off.

For those that dig into the link report for a variety of sites, this is probably more obvious.  But for those with only smaller sites, or with only a small number of sites, they might see differences as their sites grow and earn more backlinks.