my @tocheck = qw/Apple Corn Pie Fish/;
my %checkfrom = (
    Meat => {
        Fish => 1,
        Apple => 1,
        Pork => 1,
        Bacon => 1,
    },
    Fruit => {
        Apple => 1,
        Pie => 1,
        Orange => 1,
        Beef => 1,
    },
);
for my $thing (@tocheck) {
    for my $category (keys %checkfrom) {
        delete $checkfrom{$category}{$thing};
    }
}