What do you mean federating with instances that bring endless trolls, fights, spam, fascist and racist material?

All of the right-wing instances that were created housed that material and those types of users. Most instances defederated from them because of it. They did not defederate from them because they were John McCain style conservatives who wanted small government and lower taxes, they defederated from them because the admins of those instances allowed and approved of genuinely far-right fascist material and dangerous misinformation being posted there, and their users were often trolls or sealions that would mess with users on other instances.

As I responded on a different reply I gave a brief recount of my wandering onto a hexbear post not knowing they were tankies and getting mobbed by like 100 replies

That is why many instances defederated from Hexbear and Lemmygrad, including my own instance, despite being leftist itself.

But just being federated with them, their users come onto your threads and talk trash? But if not federated they can’t come onto your threads?

Yes, that’s right.

What if my instance is federated with them, and your isn’t, and we are all on the same thread on an instance we all are federated on, can they only see my replies and not yours?

Yes. I would be able to see your replies, but I wouldn’t be able to see the other comments from the defederated instance, nor would they be able to see mine.