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And finally, by "bisection", I identified the package which was causing the warning: tortoisehg (or some of its dependencies).
I had installed this package with "sudo apt-get install tortoisehg".
So now I ran "sudo apt-get install tortoisehg" from a command line and I got this prompt:
WARNING: The following packages cannot be authenticated!
tortoisehg mercurial mercurial-common
Install these packages without verification? [y/N]
Why on earth doesn't Update Manager just give the same prompt and the same Yes/No option? That's the issue.
I'll change this to Verified because I think the source of the issue is pretty clear and it's nonsense to wait for some other random person to stumble into the problem, wnich is easily reproducible.