As Roy Johnson correctly said, your first regex matches the same lines, your third matches. This doesn't happen, if you anchor the regex with /^.../ for the start of the line.

I would also do it like this to not match the second regex,when it's not appropriate:

  if (my $hit= /^port-channel (\d+)$/ .. /^\s*$/) {
    if ($hit == 1) {
      $pc_name = $1;
      next;
    }
    $Rec->{$pc_name}->{$1} = $2 if (m|(fc\d+/\d+)\s+\[(\w+)\]|); #line
+ 15    
  }
  elsif (my $hit= /^interface port-channel (\d+)$/ .. /^\s*$/) { 
    if ($hit == 1){
      $key = $1;
      next;
    }
    $hash->{$key}->{$1} = $2 if (/switchport description To (\w+) ([\d
+\.]+)/); #line 18
  }
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