I'm tempted to take this approach (assuming you're only dealing with single letter answers):

#! /usr/bin/perl
use strict;

my %test = (
question1 => 'a',
question2 => 'b',
question3 => 'a',
);

#my hash of arrays with multiple answers
my %answers = (
question1 => [
              'a'
              ],
question2 => [
             'b',
             'd'
              ],
question3 => [
             'b'
             ],
);

my $q_count = keys %answers;
my $grade = 0;

for ( keys %answers ) {
    $grade++ if "@{$answers{$_}}" =~ /$test{$_}/i;
}

print "You got $grade out of $q_count right.$/";
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