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.
I also suggest that you wait until about two weeks after you think everything has been sent and then telephone the admission office to be sure it arrived safely. (Obviously you don’t have to do this if the college has some sort of Web portal or other way of notifying applicants about materials received and you can tell that you’re all set.) But if, after waiting two weeks, you are told (either on the phone or via an applicant Web portal) that you still have missing materials, you need to re-send whatever has gone missing. The college will let you replace the lost components without penalty, if you do so promptly.
So don’t sweat a slight delay in the sending of your transcripts but do stay on top of this to make sure that the transcripts … and everything ELSE … ends up where they’re supposed to be.