Contact you dentist immediately. If you need a strong cleaning at the office it should remove the discoloration. Also if your engagers are removed the aligners can be used as whitening trays to return your teeth to a brighter whiter shade again.
Aligners will not cause an infection. You say that you brush very well, but do you also floss? Brushing cleans only one half of each tooth. Floss cleans the other half. If you are seeing pus, then you have either a gum infection from periodontitis or a tooth abscess from a dead tooth. Either way...
Your teeth look almost straight except that your lowers are slightly crowded. I have treated many such cases with Invisalign. Invisalign is the most natural way to move your teeth and I wouldn't suggest veneers as the shape and size of your teeth looks absolutely fine and they look well aligned...
