Bonding actually take work unless you are lucky. Your male rabbit is still hormonal although it has been 3 weeks since his neuter. It might take several more weeks until hormones are low.
Idon't know the age of the male but it is still common for rabbits to hump each other ; each rabbit is attempting to establish the dominant role in the relationship.
I don't know the age of your male but the female is still considered a baby. As she matures and prior to her spay she could exhibit temperamental behavior towards another rabbit especially a male.
Ideally (and even this often doesn't work) you could take your neutered male to a shelter (in a few weeks ) and allow him to pick out the female (she must already be spayed) that he prefers.
Even then when you get them home you may need to work on a bond.
The behavior that you described is normal for rabbits.
You just can't put two rabbits together and expect them to like each other. First of all they both must be fixed before you even begin and 2nd they have their preferences (just like humans) prefering one rabbit over another.
you need to read more about bonding ( info available in forum library)
http://www.rabbitsonline.net/view_topic.php?id=12072&forum_id=17
Because you already adopted the little girl I am wondering if you could have a separate habitat for her and deal with this later when the time comes ..having the rabbits live in habitats next to each other and getting used to each other.
No bond is easy except in a blue moon
if you want to try to get a mate for him immediately it is probably best for you to take her back ...
but even then you may not get the perfect mate 2nd time around