You don't need two loops because you're looking for a known key.

open(my $fh, '<', 'validate')
   or die("Unable to open validation file: $!\n");

while (<$fh>) {
   my ($name, $id) = (split);

   for my $file (keys %data) {                    
      if (exists $data{$file}{$id}) {
         print "Found $id in file $file with value $data{$file}{$id}.\
+n";
      }
   }
}
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Other problems fixed:

• Replaced globals with safer lexicals.
• Replaced 2-arg open with safer 3-arg open.
• Added error checking for open.