foreach $i(0..@hydrogen_split){             
    chomp;
    $hydrogen_split{$key}++;
}

for ( sort grep { $hydrogen_split{$key} !=1 } keys %hydrogen_split){
print "$key\n";
}
[download]

I didn't post any code. I think the code to which you refer was by borisz. Anyway, you have it a little wrong:

# loop over the array values, not indexes, making $key
# refer to each one in turn
foreach my $key (@hydrogen_split) {

# chomp is probably not needed if your data is already
# in an array.  chomp removes the end-of-line character
# from a line of input

# use the %hydrogen_split hash to keep track of which
# keys were seen how many times
   $hydrogen_split{$key}++ 
}

# print in sorted order each key that was encountered more than once
foreach my $key ( sort grep { $hydrogen_split{$key} > 1 } keys %hydrog
+en_split ) {
    print "$key\n";
}
[download]

Note that I changed his != 1 to > 1. Do you understand why?