In addition to the error pointed by Corion, I don't think you are trying to sort with the right items in the array reference you are building.

Assuming one line of your file contains something like:

12\t45
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your first map:

map {chomp;[$_,split(/\t/)]}
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will transform this line into:

["12\t45", 12, 45]
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With such data, comparing:

$a->[0] <=> $b->[0] ||
$a->[1] <=> $b->[1]
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in your sort code block makes little sense.

I would assume you probably want something like:

$a->[1] <=> $b->[1] or
$a->[2] <=> $b->[2]
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