Hashes and arrays are the same in array context. Try print join(", ", @_);at the beginning of your sub to see the effect.

I suggest passing references instead of hashes:

sub count_orientation {
    my $ref = shift;
    my $x = shift;
    my $y = shift;
    $x->{$ref}{amount}++;
    if ($y->{$ref}{orientation} eq "for"){
        $x->{$ref}{amountFor}++;
    } else {
        $x->{$ref}{amountRev}++;
    }
}
&count_orientation ($ref_end, \%error_start, \%score);
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Always remember that you're working on your original hashes when using references:

sub foo {
 my $hashref = shift;
 delete $hashref->{a};
 print keys %$hashref;
}
%x = (a => 1, b => 2);
foo(\%x);
print $x{a};
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