You misunderstand $hash{a}{b}. Hashes only have one level. $hash{a}{b} is a hash of a hash. $hash{a}{b} is a shortcut for ${$hash{a}}{b}. That means "the value at key 'b' in the hash referenced by $hash{a}." $hash{a} can't contain both a hash reference and a number, so $hash{a}++ and $hash{a}{b} conflict.

There is an easy solution. Replace

$Stats{$DestPort}++;
$Stats{$DestPort}{covert}{"..."}++;
[download]

with

$Stats{$DestPort}{total}++;
$Stats{$DestPort}{covert}{"..."}++;
[download]

or

$Stats{$DestPort}{total}++;
$Stats{$DestPort}{item}{covert}{"..."}++;
[download]