use strict;
use warnings;
...

open MATCHING_FILE, $TEXT_FILE;
my %seen;
while (my $file = <MATCHING_FILE>){
    chomp $file;
    if ( $file =~ /[\d]{1,3}\.[\d]{1,3}\.[\d]{1,3}\.[\d]{1,3}|password
+|(ssn=)/i){
        $seen{$file}++;
    }
}

print "$_\n" for keys %seen;
[download]

Your code won't work because you'r asigning to %hashTemp for each iteration, thus deleting all previous entries.

Update: fixed copy&paste error, Roy Johnson++