Unless you're messing with $/ or $\, chomp will remove the newline, and there cannot possibly be two of them.
Your code does exactly what you say you want it to do.
while(<DATA>){
chomp(my $record = $_);
my @field = split /\,/, $record;
print "$field[0],$field[10],$values[0],$field[1],$field[2]\n";
}
__DATA__
a,b,c,d,e,f,g,h,i,j,k
a,b,c,d,e,f,g,h,i,j,k
a,k,,b,c
a,k,,b,c
There's an empty field, but that's because I didn't give $values[0] a value. (In fact, I would get a warning with use warnings;.)
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