Maybe I'm not getting what you mean but I think you are not understanding pattern matching correctly.

Can someone tell me why it is matching the . or the - at the end of the line?

In both cases, the last character is not matched by the regex!

if ($domain =~ /[A-Z0-9]+[A-Z0-9-]+[A-Z0-9]/i) {
  # do A
} else {
  # do B
}
[download]

does A or B depending on whether the pattern matched the string $domain or not. It does not change $domain in any way, however. And your pattern does not have to match the whole string:

# /[A-Z0-9]+[A-Z0-9-]+[A-Z0-9]/i matches
someDomain
someDomain..
..someDomain..
_!@#!@#!@#01a!@#$
# and so on
[download]

If you are interested in what was matched, you have to use capturing parentheses like this:

if ($domain =~ /([A-Z0-9]+[A-Z0-9-]+[A-Z0-9])/i) {
  # $1 contains what is in the first pair of parentheses
  print "$1 matched\n\n"; 
} else {
  print "$domain did not match\n\n";
}
[download]

Play around with this code and different pattern. Furthermore include the assertion ^ and $ into the pattern as mentioned by OeufMayo and play some more.

-- Hofmator