Include word boundaries in the patterns.

my @phrases = ( 'pail of water', 'pale horse' );
my $phrases_re = join '|', map { "\\b$_\\b" }
                           map { quotemeta } @phrases;
foreach my $sentence ( @sentence_source ) {
    $sentence =~ s/($phrases_re)/\#$1\#/g;
}
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(Note the extra map.)