Colleges expect the part of the application that comes from YOU to arrive by the deadline (and this includes financial aid forms, too, when required). But if a part that comes from elsewhere (counselor forms, transcript, teacher recommendations, test scores) shows up a bit late, it will not be a problem for you. It always takes the admission office secretarial staff quite a while (as much as a couple weeks) to process all of the materials that arrive right around the deadline time. So even materials that do show up on time may not reach a student’s application folder until 10 or more days later.
Meanwhile, keep checking Naviance to make sure that the transcript status changes. If, after a few days, it still says, “Requested,” go speak to your counselor in person.