The following works:

use strict;
use warnings;

my @phrases=('(arf)71', 'p65(91)', 'H:223', 'Phospholipase A2 inhibito
+r', 'Phospholipase A2', 'Phospholipase', 'PLI-A', 'PLI-B', 'PLI');

my $string = join '|', map { quotemeta } @phrases;

my $in = "(arf)71 p65(91) H:223 Phospholipase A2 inhibitor ( PLI ) , p
+urified from the blood plasma of the Habu snake ( Trimeresurus flavov
+iridis ) , was separated into two distinct subunits , PLI-A and PLI-B
+";

my $out = "#(arf)71# #p65(91)# #H:223# #Phospholipase A2 inhibitor# ( 
+#PLI# ) , purified from the blood plasma of the Habu snake ( Trimeres
+urus flavoviridis ) , was separated into two distinct subunits , #PLI
+-A# and #PLI-B#";

#while($in =~ s/(^|\s)($string)(\s|$)/$1#$2#$3/) {};
while($in =~ s/(^|\s)($string)(\s|$)/$1#$2#$3/g) { pos() = pos() - 1; 
+};

print "success!!\n" if($in eq $out);
print "in: $in\n";
print "out: $out\n";
[download]

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

my $phrases_pat = join '|', map quotemeta, @phrases;
$in =~ s/(?<!\S)($phrases_pat)(?!\S)/#$1#/g;
[download]

Bonus: In addition to being much simpler, this should be faster since much less work is outside the substitution, in matching and in replacing.