I believe it is because your %two hash contains as values references to the same anonymous arrays as are in %one. You would have to do something like (not tested)

my %two;
foreach my $key ( keys %one )
{
    $two{ $key } = [ @{ $one{ $key } } ];
}
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in order to create values which are new anonymous arrays containing the same contents as those in the original hash.

I hope this is helpful.