#
# 5x5 map grid for each player
# Cruiser = *
# Carrier = @
# Submarine = ~
# Ocean/Empty Space = .
[download]

Your grid is actually 10x5.

# Stats trackers
my @p1Attacks;
my @p2Attacks;
[download]

The variable @p2Attacks is never used anywhere so it could be removed.

# Ships - surely there is a better way to do this
my %p1cruiser = ( 'hp' => '2', 'size' => '3', 'ap' => '1', 'loc' => ''
+, 'sym' => '*', 'mc' => 0 );
my %p1carrier = ( 'hp' => '3', 'size' => '5', 'ap' => '2', 'loc' => ''
+, 'sym' => '@', 'mc' => 0 );
my %p1subm    = ( 'hp' => '1', 'size' => '2', 'ap' => '3', 'loc' => ''
+, 'sym' => '~', 'mc' => 0 );

my %p1ships = ( 'cru' => \%p1cruiser, 'car' => \%p1carrier, 'subm' => 
+\%p1subm );

my %p2cruiser = ( 'hp' => '2', 'size' => '3', 'ap' => '1', 'loc' => ''
+, 'sym' => '*', 'mc' => 0 );
my %p2carrier = ( 'hp' => '3', 'size' => '5', 'ap' => '2', 'loc' => ''
+, 'sym' => '@', 'mc' => 0 );
my %p2subm    = ( 'hp' => '1', 'size' => '2', 'ap' => '3', 'loc' => ''
+, 'sym' => '~', 'mc' => 0 );

my %p2ships = ( 'cru' => \%p2cruiser, 'car' => \%p2carrier, 'subm' => 
+\%p2subm );
[download]

The hashes %p1cruiser, %p1carrier, %p1subm, %p2cruiser, %p2carrier and %p2subm aren't really needed:

# Ships - surely there is a better way to do this
my %p1ships = (
    cru  => { hp => 2, size => 3, ap => 1, loc => '', sym => '*', mc =
+> 0 },
    car  => { hp => 3, size => 5, ap => 2, loc => '', sym => '@', mc =
+> 0 },
    subm => { hp => 1, size => 2, ap => 3, loc => '', sym => '~', mc =
+> 0 },
    );

my %p2ships = (
    cru  => { hp => 2, size => 3, ap => 1, loc => '', sym => '*', mc =
+> 0 },
    car  => { hp => 3, size => 5, ap => 2, loc => '', sym => '@', mc =
+> 0 },
    subm => { hp => 1, size => 2, ap => 3, loc => '', sym => '~', mc =
+> 0 },
    );
[download]

    # Get in use tiles for ship hashes
    foreach my $ship ( keys %p1ships ) {

        if ( ! $p1ships{$ship} ) {
            next;
        }
        my $shipRef = $p1ships{$ship};
        my $location = ${$shipRef}{loc};
        my @inUseTiles = split(",", $location);
        foreach my $iut ( @inUseTiles ) {
            push(@p1usedTiles, $iut);
        }
    
    }
[download]

push is a list operator so you don't need a foreach loop.   And you don't really need all those intermediary variables.

    # Get in use tiles for ship hashes
    foreach my $ship ( keys %p1ships ) {

        next unless $p1ships{ $ship };
        push @p1usedTiles, split /,/, $p1ships{ $ship }{ loc };

    }
[download]

sub checkLocation {

    # Given a set of coordinates, determine if they are already occupi
+ed
    my $taken = 0;
    my $coordinates = shift;
    if ( $coordinates !~ /^[0-9]*,[0-9]*$/ && $coordinates !~ /^[0-9]*
+,[0-9]*,[0-9]*$/ && $coordinates !~ /^[0-9]*,[0-9]*,[0-9]*,[0-9]*,[0-
+9]*$/ ) {
        print "These coordinates look incorrect, you shouldnt see this
+ error...\n";
        $taken = $taken + 1;
    }

    my @coors = split(/,/, $coordinates);
    foreach my $coor ( @coors ) {
        if ( $p1map{$coor} ne "." ) {
            print "coordinate $coor contains $p1map{$coor}\n";
            $taken = $taken + 1;
        }
    }

    if ( $taken >= 1 ) {
        return 1;
    } else {
        return 0;
    }


}
[download]

You are checking $coordinates for either one, two or four commas, with optional numbers.   Perhaps you should change [0-9]* to [0-9]+.

$taken = $taken + 1 could be shortened to $taken += 1 or even ++$taken.

The return code could be shortened to return $taken >= 1 ? 1 : 0 or even return $taken >= 1.

    # Get random ship key and href
    my @availShips;
    foreach my $key ( keys %p2ships ) {
        if ( ! defined $p2ships{$key} ) {
            next;
        } else {
            push(@availShips,$key);
        }
    }
[download]

That can be shortened a bit:

    # Get random ship key and href
    my @availShips = grep defined( $p2ships{ $_ } ), keys %p2ships;
[download]

    # Make sure AI doesn't try to 'move' if it has no available moves 
+left
    print "Checking available AI moves\n";
    my @availMovers;
    foreach my $key ( keys %p2ships ) {
        my $shipRef = $p2ships{$key};
        if ( ! defined $p2ships{$key} ) {
            next;
        } elsif ( ${$shipRef}{mc}  == 1 ) {
            next;
        } else {
            push(@availMovers, $key);
        }
    }
[download]

Same as with above:

    # Make sure AI doesn't try to 'move' if it has no available moves 
+left
    print "Checking available AI moves\n";
    my @availMovers = grep defined( $p2ships{ $_ } ) && $p2ships{ $_ }
+{ mc } != 1, keys %p2ships;
[download]

# Menu loop
while () {

    my $count = 0;
    if ( $count == 0 ) {
        &printMenu;
    }

...

    $count++;

}
[download]

The $count variable should be defined outside the loop if you want it to work correctly:

# Menu loop
my $count = 0;
while () {

    if ( $count == 0 ) {
[download]

&printMenu should be printMenu().

            my @opponentRemaining;
            foreach my $key ( keys %p2ships ) { 
                if ( defined $p2ships{$key} ) 
                    { push(@opponentRemaining, $key) 
                } 
            }
[download]

Same as with above:

            my @opponentRemaining = grep defined( $p2ships{ $_ } ), ke
+ys %p2ships;
[download]

                my @validInputs;
                foreach my $key ( keys %p1ships ) {
                    my $shipHref = $p1ships{$key};
                    my $moveCounter = ${$shipHref}{mc};
                    if ( ! defined $p1ships{$key} ) {
                        next;
                    } elsif ( $moveCounter == 1 ) {
                        next;
                    } else {
                        push(@validInputs,$key);
                    }
                }
[download]

Same as with above:

                my @validInputs = grep defined( $p1ships{ $_ } ) && $p
+1ships{ $_ }{ mc } != 1, keys %p1ships;
[download]

Dereferencing like ${$shipHref}{mc} are usualy written as $shipHref->{mc}.