no warnings qw /uninitialized/;

I guess you've put it specially to silence the exact warning that tells you where the error is. You're splitting on "\t", but looking onto your input I have the impression that there are no tabs. So $value in

next if $value > 500;

is probably uninitialized.

Update: well, after looking more closely I think real input contains tabs, but then it should work (to some extent). I think it is was a rather weird idea to keep coordinates in array like you did, e.g. you don't have 0 element, and some others may be missing. Here's a simplified version:

#!/usr/bin/perl
use Modern::Perl;

while (<DATA>) {
    chomp;
    my ($index, $value) = split /\s/;
    say "$index\t$value" if $value <= 500;
}

__DATA__
1 10
2 11
3 9
4 500
5 550
[download]

Update: removed unused var