The Perl::Critic policy in question is Perl::Critic::Policy::ControlStructures::ProhibitMutatingListFunctions. It implements the policy recommendation from page 114 of PBP, which suggests that if you really need to do what you're doing, make a lexical variable.

my @files
    = map {
        my $file = $_;
        chomp $file;
        $file =~ s{ \A \s+ | \s+ \z }{}xmsg;
        $file;
    } <$FILES>;
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It goes on to say that if you really do want a side-effect of your loop, use for instead.

Perhaps merlyn's use of local (as in modifying $_ in map (was Re: A perverse use of grep)) should be allowed by the policy. I don't think so, but I could see that being an option. In any case, rt://Perl::Critic might be a good place to make that case.