That's an excellent point actually. I'll amend my answer, although I covered it somewhat. Assuming you actually trust the user, this seems like a sane way to do it.

my $regexp = <$file_handle>;
my $creg   = eval { qr($regexp) };

if( $@ ) {
   warn "regex error: $@";

} else {
   if( $something =~ $creg ) {
      # do wonderful things.
   }
}
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I apparently skipped the meat of the question because it seemed clear to me that the reason the matching failed was because of an interpolation problem with a test regexp that he generated between quotes and he wasn't actually reading it from the user -- which would have likely worked the way he had it.