Well, if you're using the prepared statement only once, it's not clear how much benefit you're getting from it.
Nevertheless, if you want to do it that way, you need as many placeholders as values:
my $sql = qq{
SELECT COUNT(*)
FROM some_table
WHERE some_column IN (} . join(',', (('?') x @values)) . ")";
To me the "better" way would be to prepare the statement once and execute in a loop:
my $sql = <<END_SQL;
SELECT COUNT(*)
FROM some_table
WHERE some_column = ?
END_SQL
my $sth = $dbh->prepare_cached($sql) || die;
foreach my $value (@values)
{
$sth->execute($value);
while ($sth->fetch)
{
# etc.
But it sounds like you've already thought of that.
HTH