How late was it? This stuff happends all the time. Most likely they will just count you a part of R3 with everyone else and you'll never have to think about it again. It's really not such a big deal. I know it makes you feel like you did something wrong, but in fact it was just a mistake/glitch on the part of your recommender. It will not reflect poorly on you, and it will probably be no biggie. So don't lose sleep over it. The strict deadline is usually only held for submission of the application itself, and even then there is a little bit of buffer room. Let us know how it turns out