The distinguishing factor is that a hyphen and a digit follow the name you are looking for.

use strict;
use warnings;

my @array1 = qw/ cups-1.5.2-9.fc16.x86_64 cups-libs-1.5.2-9.fc16.x86_6
+4 cups-1.5.2-9.fc16.x86_64/;
my @array2 = qw/ cups-libs-1.5.2-9.fc16.x86_64 cups-libs-1.5.2-9.fc16.
+x86_64 /;
my $pattern = "cups";

print "Array1:\n", join "\n", grep { /^$pattern\-\d/ } @array1;
print "\nArray2:\n", join "\n", grep { /^$pattern\-\d/ } @array2;
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