It is up to the program to decide how much leniency to give for late transcripts and references. If you have applications due and still don't have LOR's I would recommend calling your letter writers ( NOT emailing).
I have heard of late transcripts twice. Each time we asked the student what date they submitted. On one the university dropped the ball and we got it a couple of days late. On the other the student didn't submit the request until after Christmas. We marked theirs as incomplete.