I had the gawd awful experience just the other day of having an adult male rat basically castrate a male cage mate so believe me you'd know if that had happened (think blood, stuff hanging out and well, enough said...there's no way you wouldn't notice).

Young male rats can retract their bits quite a lot, not so much as they get older, breed more and basically grow pretty large butt pillows. Check a male by picking him up with your hand basically around him under his "armpits" (head up), let his butt end dangle. That should drop everything he has back into visible position. I check all potential male breeders this way - I don't waste my female time on males that don't have what it takes LOL.

Female rats can turn on a male sometimes. As Bruce said I had a male rat darn near ripped to pieces last year by an aggressive female. They'd both bred before but for some reason she went looney tunes on him that time around. He survived - she became boa food (I don't keep nasty or unstable tempered rats).