The Total Reputation counts on the Reputation League pages appear to be somewhat wonky.
You should be able to reproduce it on any StackExchange Reputation League, but here I'll use the numbers from the Anime & Manga Stack Exchange League page. On the right are two tables, the bottom of which is Total Reputation. Basically, each level seems to accumulate; our five 5k+ users count in the 3k+ group as well, for example. (If this was not the case, we should have only five 3k+ users counted.)
However, some of the counts appear to be wrong. It says we have only 35 users with 500+ rep, but we actually have 41 (an undercount of 6). The 200+ count says we have 62, but in reality we actually have 98 (which, incidentally, is reported correctly by our Area 51 site).
Here is the full table of the reported counts by the league, and the actual counts I found by looking at our Users page:
Label | League Count | Real Count (from Users)
-------+---------------+-------------------------
5,000+ | 5 | 5
3,000+ | 10 | 10
2,000+ | 12 | 13
1,000+ | 22 | 22
500+ | 35 | 41
200+ | 62 | 98
1+ | 760 | 851 (Area 51 says 906)
I have a suspicion that this is related to the association bonus. However, these bonuses do seem to count on leagues, so this shouldn't have any bearing on it. (Here is an example on Sustainable Living; #4 has an association bonus on Jun 4th that is counting for the week of Jun 2, 2013 - Jun 8, 2013.)
I've crossed out the above as it has been explained in the comments. The information below still has not been addressed and appears to be a bug.
The 760 for the 1+ users also seems to be calculated very oddly: If we take the total user count (906) and subtract all the other entries (5 + 10 + 12 + 22 + 35 + 62 = 146), we get (906 - 146) 760. This is not only incorrect (as it would be adding all the 5k+ users 6 times), but it's just easier to pull the count of 906 since all users have 1+ rep.
(NB: This anomaly has another semi-obvious effect: For example, April 2013 had 756 1+ users, whereas May 2013 somehow went down to 749. June has taken us back up to 760.)
