From the instructions, I think it is the confusion on what active vs inactive thoughts meant. Also, I wasn't sure if the text sometimes was white or grey, but that might be more of a "my eyes are only so-so" thing.
My big question when playing was why some things would connect and others would not. It didn't really click when I was playing through experimentation. I understood the "..." needed something after it, from the instructions, but I could connect two things without any "..."'s. And sometimes a connection wouldn't link and there was no real feedback on why.