We had that when we kept one of a litter. Mother cat occasionally attacked the kitten but most of the time she just looked at him with a 'WTF expression'. There is nothing like a cat for expressing utter disgust. The kitten grew quickly and was soon able to give as good as he got and they settled down happily together.
Our cat had 2 litters of kittens and rejected them both (long story, 15 kittens in total) and lost them all bar one which we hand reared. He thinks he's a human in a cat jacket, or we're cats in human jackets and he and his mother really, really don't get on. Every time she goes past him she hums at him, and he tries to bully her half the time. Every now and then they forget and curl up together but most of the time they lead separate lives. They're happy to eat at the same time, but generally have different hanging out places and avoid each other.
She's probably telling him that it's her house and it's time to move on, but once she realises that kitty is staying I expect she'll begrudgingly be ok. Being spayed may help, I would just work on keeping them separate when possible for their peace of mind and let them work it out, if necessary when kitty is a bit bigger!