You're putting stuff in the anonymous array (potentially) twice:
$hash{$arg} = [@array];
push (@{ $hash{$arg} }, @array) unless /^\#|none|unkno/i;
The first line copies all of the contents of @array and populates an anonymous array with them, sticking it in the hash slot.
The second pushes all of the elements of @array onto the anonymous array, unless your regex matches. (Which it probably won't.)
I'd do something like:
while (<FILE>) {
next if /^#/;
next if /none|unkno/i;
chomp;
# print "$_\n"; returns expected results
my @array = split;
# printing each array element also passes here
$hash{$arg} = [@array];
}