The error occur because you're are only initializting $a. Try:

my ($a,$c,$g,$t) = (0, 0, 0, 0);
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or

my $a = 0;
my $c = 0;
my $g = 0;
my $t = 0;
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Notice the lack of quotes around a numerical zero.

Aside from that,

• you have lots of redundancy,
• you use the less readable form of for,
• you use $a which is special, and
• you use four seperate vars ($a,$c,$g,$t) where a hash would be better.

Fix:

sub comNucCount {
    my($string1, $string2) = @_;
    $string1 = uc $string1;
    $string2 = uc $string2;

    my %counts = map { $_ => 0 } qw( A C G T );

    for my $position (0 .. length($string1)-1) {
        my $char = substr($string1,$position,1);
        $counts{$char}++
            if substr($string2, $position, 1) eq $char;
    }

    return "A=$counts{A}, C=$counts{C}, G=$counts{G}, T=$counts{T}";
}
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