Hi Alex,
I had also submitted this to the Wordfence forum: https://www.ads-software.com/support/topic/supercache-file-critical-warning/
In short, it appeared to me that it was code held on the cache. Once cleared, there were no issues until hours later when the code re-appeared.
I finally deleted Supercache and that resolved the issue. (I also followed the Wordfence steps to take if you think your site might be infected.)
Hope this helps,
