The last semicolon is between 2105 and 2123. So split stuffs everything after the last semi into $fields[6], namely "2123 0 chr5 75483987 0 82M3I16M * 0 0". You need to do more work to get the number you want from $fields[6]:

use warnings;
use strict;

while (<DATA>) {
    my $line = $_;
    if ( $line =~ /^HWI/ ) {
        my @fields = split /:/, $line;
        my ($f6) = $fields[6] =~ /(\S+)/;
        print $fields[5], " ", $f6;
    }
}
print "\n";

=for output

2105 2123

=cut

__DATA__
HWI-1KL120:99:C0C9MACXX:6:1101:2105:2123 0 chr5 75483987 0 82M3I16M * 
+0 0
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