pos() = pos() - 1;? ow! Use zero-width matches.

my $phrases_pat = join '|', map quotemeta, @phrases;
$in =~ s/(?<!\S)($phrases_pat)(?!\S)/#$1#/g;
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Bonus: In addition to being much simpler, this should be faster since much less work is outside the substitution, in matching and in replacing.