I don't think there's anything to fix in cvmfs regarding this, but for documentation purposes, last week I saw the following /var/log/messages entries:
The squid in use for this case was a single machine squid.fnal.gov, but it has multiple workers that cache things independently. The stratum 1 is a single machine with a squid on it which also has multiple workers and which does not cache but forwards everything to an apache on the same machine. After following through all the log entries I came to the conclusion that it was most likely a problem in the squid-3.5.x installed on squid.fnal.gov, and filed a bug report with the squid project. It appears that squid is sending If-Modified-Since with some timestamp that it guessed at even though there was no Last-Modified field, and it guessed wrong.