To my mind, Moodle is giving exactly the right information - the final version of the assignment that the student submitted (and which is being marked) was submitted after the deadline. If the date shown was the first date anything was submitted, then a student could simply upload a blank document (to meet the deadline) and then submit the final assignment when they got around to it.
If you want to ensure that students don't change anything after they have finished submitting, then the 'require students to click on submit for marking' feature will mean that everyone is clear about when the student submitted the final piece for marking.
The new feature in Moodle 2.5, related to resubmissions, is that once a teacher has marked an assignment, it is possible to allow the student to resubmit their work (and then again after the next marking, if the teacher allows it). This keeps a history of the submissions and grades, but only at the point where each submission is marked (it would be confusing to add to the submission history for each time a student uploads a single file).