I think your problem seems not being caused by the code you show us. It is probably caused in the construction the arrays. You might have used the method below:

$array2[$n] = $array1[$n];
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Because your two arrays are complex, this does not copy the structure and content, but only copy the corresponding reference. So the value $n in @array2 actually points to the value $n in @array1.
In addition, while asking questions, please make your code more refined, for example:

for my $i (0..$#array1) {
    for my $j (0..$#array2) {
        # do something
    }
}
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