Lemon is not a Cottontail. A Cottontail wouldn’t have the white fur around its neck and on its face. Also, a Cottontail, unless it was very sick or injured, would not have allowed someone to just pick it up and take it to a shelter.
Was Lemon just recently spayed? If so, you should wait a month before starting the bonding. And she needs some settling in time. The fact that there was no fighting when you put the rabbits together is good. It’s not uncommon for one of the rabbits to ignore the other. She may have been frightened and didn’t want anything to do with another rabbit, or she just may not know how to interact with another rabbit.
If enough time has elapsed since her surgery, keep trying with the bonding. I have always had success putting the two rabbits in an x-pen, and my husband and I get in with them. You can be there to comfort any rabbit that might need it, you can stop any fighting (some scuffling can be normal) and you can stop the humping if it goes on too long.
Bonding can take time, so you have to have patience and you may have to try different methods.
Here are 2 good articles:
https://binkybunny.com/BUNNYINFO/tabid/53/CategoryID/9/PID/940/Default.aspx
http://rabbit.org/faq-bonding-multiple-rabbits/