Currently there's no mechanism for refreshing category member counts. So certain categories, like http://en.wikipedia.org/wiki/Category:Temporary_Wikipedian_userpages say they have over 12,900 members, when in reality it has only about 3,000 members.
populateCategory.php is a bit of a brute-force approach (it recalculates everything, even categories whose counts are correct). We could do with another script that specifically recalculates wrong counts in the category table.
T85696 is about adding a way for users to invoke recounting when required.