I have 14 years in the Army. I have heard of only a handful of sexual assault cases. I know quite a few women in the Army and not one I have known has been raped, and I know a lot more then 10.
I have heard of the 1 in 3 number, but it has really only come from one source.
I have seen a lot of cases were a female accused a male of rape when they got caught in a place where sex was not allowed. It was all concensual until they got caught. I am not saying it doesn't happen, but I have seen this more then I have seen an actual assault.
While I was stationed on a Navy ship one time, the females on the ship had formed a prostitution ring. They tried to claim rape right up until the record book was found for transactions.
To stop it, education is about the only thing you can realistically do, which is what we do in the Army. Males need to be informed of the correct things, punishments and prevention methods. For females the biggest thing is stay with a battle buddy. Even the battle buddy thing is only so good because there have been cases of female on female rape as well.
The other methods would be to completely separate males and females, which the ACLU, NOW and others would condemn. Even then you could still have female on female.
The place I have seen it the highest was in basic training, in the reception unit, before the female trainee oficially started basic training. The handful of actual assault cases I have seen was in basic training, before they get their first classes about UCMJ and their rights.
Male on male assault cases have gone up since Dont Ask Dont Tell, but these are rare and generally not talked about for a variety of reasons.