... if you factor out the common \s.

my $string = join '|', map {quotemeta} @phrases;
$sentence =~ s/(\s$string\s)/#$1#/g;
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But if  @phrases was something like  qw(foo bar baz) then the final substitution regex would be equivalent to
    $sentence =~ s/(\sfoo|bar|baz\s)/#$1#/g;
in which a leading space is associated only with  foo and a trailing space only with  baz and nothing with  bar.

Adding a non-capturing sub-grouping should do the trick:
    $sentence =~ s/(\s(?:$string)\s)/#$1#/g;