Correct me if I'm wrong, but it seems that negative scores are produced only with Multiple Choice Single Answers (radio-buttons) ? And NOT when we allow more than one answer (checkboxes) ? In the latter case the Quiz reports of various kinds also show zero even if the raw sum total should be less, mathematically.
Such at least has been my experience so far. And this inconsistency is causing us to think of tweaking the quiz code to force a consistent behaviour (no negative scores) when single answers are used.
Also, not sure only Deferred feedback is affected; I've been testing this "problem" using the Adaptive mode without penalties.
Here below are two screnshots illustrating my experience:
ONE ANSWER CASE:
MULTIPLE ANSWERS ALLOWED CASE - this for me is the expected quiz behaviour by default:
GRADEBOOK shows zero in both cases (OK with me !) :
Regards.