One issue I've had with WeBWorK, but admittedly have never done anything about, is that submissions that aren't recorded for credit don't get logged at all. This means that if a student clicks "Grade Test" too late, they get a message saying that their submission wasn't recorded, but there's no record on the server that they even submitted.
It should be an easy fix to have these recorded to the answer log. At least that way the instructor has something to work from if there is no submission. Alex's suggestion is a better way to go, but as he says it's more work.