The problem arises in this line  my $n = $.;. $. (also known as $INPUT_LINE_NUMBER. See perlvar), is the record or line number of the last line read from a file.

In the original code that line came immediately after the while( my $line = <DATA> ) { loop, so $n was set to the number of lines in the file.

In your code/function, you are not reading from a file, therefore $. is 0, so $n gets set to 0, hence the error in this line:

$_ = map { $_ ? $_ / $n : 0 } @$_ for values %pwm;  # Line 26
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As you are passing the data into the function as a list and assigning it to an array, the equivalent value is the number of elements in the array. Eg. scalar @data;. So, modifying your code as

use Data::Dumper;

my @inst = ( 'AAA', 'ATG', 'TTT', 'GTC' );
get_pwm(@inst);

sub get_pwm {

    my @data = @_;
    my %pwm;
    foreach my $line (@data) {

        ++$pwm{ substr $line, $_, 1 }[$_] for 0 .. length($line) - 1;
    }

    my $n = @data; ### Modified
    @$_ = map { $_ ? $_ / $n : 0 } @$_ for values %pwm;  # Line 26

    print Dumper \%pwm;
    print "$_ => @{ $pwm{ $_ } }" for keys %pwm;

    return;
}
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Produces this output (assuming -l):

$VAR1 = {
          'A' => [
                   '0.5',
                   '0.25',
                   '0.25'
                 ],
          'T' => [
                   '0.25',
                   '0.75',
                   '0.25'
                 ],
          'C' => [
                   0,
                   0,
                   '0.25'
                 ],
          'G' => [
                   '0.25',
                   0,
                   '0.25'
                 ]
        };

A => 0.5 0.25 0.25
T => 0.25 0.75 0.25
C => 0 0 0.25
G => 0.25 0 0.25
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Not sure why you are outputting the results two different ways. It's also not typical to output from within a subroutine.