Kirsten,
I am not sure wether you've mentioned it, but is Lily spayed already?!

As Luna always felt a bit like Lily's mom that could be one of the reasons...because as soon as "their" kittens come into heat the mothers often refuse close contact with them...in the wild this is the moment when the youngsters are send out to find their own territories...
An intact male or female is almost always superior to spayed/neuterd cats in the pecking order and that might arise some conflicts between them?!