If a throttle and warning is enabled on filter, the edit is counted also when the warning is shown. I think it should only count for the limit if an edit is taken or denied and not on warning, because the user sometimes don't know that he isn't allowed to take this action before he has read the warning message.
Counting at denied action (after warning) could be useful because at that time the user should known what he does.
See Also: T49493