This is currently my flagging history in Physics.SE:
As you can see, 235+6+8=249 and not 250. In addition, I don't have any pending flag (so this is not a duplicate of this question). Where is the missing flag?
Well this is a weird edge case and the flag involved isn't getting included in the total because your flag was invalidated by an event. The flag is listed on your history page, it's just not covered in any of the categories for filtering.
The timeline for this was:
removed during a deletionof the post.
If you look at your flag history page, you will see the flag and the resolution of the flag. As I said, this is a weird edge case and we don't have a category for these flags to filter on. I'll look to see if this is happening on a frequent basis to see if we need to consider adding a weird edge case type of category for these one-off flags, but I doubt it's happening enough to make a change.