lightoverhead is correct. Perhaps you missed the "g" modifier? There will be three matches.

1. $1 = substr($chr, 0, 4); $2 = undef;
2. $1 = undef;              $2 = substr($chr, 5, 3);
3. $1 = substr($chr, 9, 4); $2 = undef;

Update: I understand your confusion better now. I'll correct what you said:

$1 represents what was matched in the first set of matched parenthesis. $2 represents what was matched in the second set of matched parenthesis.

There's no such thing as "matched parentheses" Either the whole pattern matches or it doesn't.

   ________ $1 unconditionally refers to this capture
  /         if the match was successful.
 |
 |       __ $2 unconditionally refers to this capture
 |      /   if the match was successful.
 |     |
 v     v
/(...)|(...)/
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It can easily be demonstrated:

for (qw(a b)) {
   /(a)|(b)/;
   print(
      defined($1) ? $1 : '~',
      defined($2) ? $2 : '~',
      "\n"
   );
}
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a~
~b
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