Your rules for what you count are a little strange, but this produces the same result.

Update 1: No it doesn't! You caught me out with the duplication of value 43 in @all_data.

Is it any better?

C:\test>p1
use List::Util qw[ sum ];;

@selected_data = qw(13 76 90 13 77 100 76 300 13 65 400 74 89 34 65);
@all_data = qw(1 5 2 8 12 87 13 76 98 77 89 90 11 65 43 74 43 32 34 67
+);;

++$seen{ $_ } for @selected_data, @all_data;;

print sum map{ $_ > 1 ? $_ - 1 : () } values %seen;;
13
[download]

Update2: This is better.

@selected_data = qw(13 76 90 13 77 100 76 300 13 65 400 74 89 34 65);
@all_data = qw(1 5 2 8 12 87 13 76 98 77 89 90 11 65 43 74 43 32 34 67
+);

@seen{ @all_data } = ();;

exists $seen{ $_ } and $count++ for @selected_data;;

print $count;;
12
[download]