You're putting stuff in the anonymous array (potentially) twice:

$hash{$arg} = [@array];
push (@{ $hash{$arg} }, @array) unless /^\#|none|unkno/i;
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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];
}
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