2 months of intros

I got a new kitten 2 months ago I kept them separate for a month and did the whole scent swap, swapped spaces and fed near each other and played with at the same time. Now I’ve let the little guy roam free while we’re at home. My girl cat 80% ignores him. Doesn’t care about him, eats while he’s around, they use the same litter box now. But the 10% she hisses, growls and hits him. He hides from her in a cat house or I’ll pick him up and carry around like a baby which he loves.

I guess I’m wondering if this because she’s being territorial and he’s in her space like playing with her toys and being around us. We play with both of them. I make sure to fed them together and do treats together. Any help is appreciated!