"Tons" is the clue. Perhaps they were sitewide links somewhere and that site has removed the links. Perhaps they were forum signatures and old posts have been archived/removed.
If they were tons of unique links from individual sites, it's an algo catching up with a particular linking practice. For example, a thin affiliate site with a thousand IBLs is "probably" a self-initiated linking pattern.
Slowly, Google seems to be catching up with abnormal linking patterns.