my $data;
my $sorted;

while( <> ) {
 my @cols = split /,/, $_;

 for my $i ( 0 .. $#cols ) {

#counter for the unique element
 $data->[ $i ]->{ $cols[ $i ] }->[ 0 ]++;

#undefine the array element in sorted if a $data reference was previously defined
 undef $sorted->[ $i ]->{ \$data->[ $i ]->{ $cols[ $i ] }->[ 1 ] } if
$data->[ $i ]->{ $cols[ $i ] }->[ 1 ];

#elements in $sorted
 my $stack = $#{ $sorted->[ $i ] };

#store the new reference to the $data record at the top of $sorted's stack
 $sorted->[ $i ]->[ $stack ] = \$data->[ $i ]->{ $cols[ $i ] };

#reference to place in $sorted so that it may be undefined later if necessary
 $data->[ $i ]->{ $cols[ $i ] }->[ 1 ] = \$sorted->[ $i ]->[ $stack ];

 }
}

#then, you could just loop through sorted. bypassing:
# sort { $data->[ $i ]->{ $a } <=> $data->[ $i ]->{ $b }
# } keys %{ $data->[ $i ] }
# with something like

for my $i ( 0 .. $#{ $sorted } } ) {
 foreach my $j ( 0 .. $#{ $sorted->[ $i ] } ) {
 print "column ". $i . ":" . $sorted->[ $i ]->[ $j ]->[ 1 ] . " had "
. $sorted->[ $i ]->[ $j ]->[ 0 ] . " duplicates\n" if( $sorted->[ $i
]->[ $j ] );
 }
}