I'm not sure I can help with the overall problem, but I do have some suggestions.

change the regex to use the $line variable instead of the default $_.

$line =~ /^(\d{1,2})$/;
$points[$1] = 1;
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In place of your for loop, I would suggest using a simple foreach. You don't seem to be using the $i variable anyway. If you want to keep the for loop, you'll need to change it to

for ( my $i = 0; $i < scalar @points; $i++ )
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I hope this helps.