1. chomp doesn't return the modified string, it changes the argument in place.
2. xpoints needs a sigil.
3. Spaces aren't needed before semicolons.
4. Numbers don't need double quotes.
5. The actual number of elements is ($xpoints + 1) * ($ypoints + 1) - 1 because you start at 0, 0.

#! /usr/bin/perl
use warnings ;
use strict ;

print 'Last X Point' , "\n";
chomp( my $xpoints = <STDIN> );

print 'Last Y Point' , "\n";
chomp( my $ypoints = <STDIN> );

my %position;

my $key = 'a';
for my $y (0 .. $ypoints) {
    for my $x (0 .. $xpoints) {
        $position{$key++} = [$x, $y];
    }
}

for my $key ('a' .. $key) {
    print "'$key' => [$position{$key}[0],$position{$key}[1]],\n"
        if $position{$key};
}
[download]

'a' => [0,0],
'b' => [1,0],
'c' => [2,0],
'd' => [3,0],
'e' => [0,1],
'f' => [1,1],
'g' => [2,1],
'h' => [3,1],
'i' => [0,2],
'j' => [1,2],
'k' => [2,2],
'l' => [3,2],
'm' => [0,3],
'n' => [1,3],
'o' => [2,3],
'p' => [3,3],
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]