Spoiler!
As far as the Clark/Lois dynamic goes, my impression was there was lengthy conversation offscreen between the two that took place between the moment he met her at his father's grave and told her about his death, and when he shows up at the farm and tells Martha "she's a friend".
Maybe it needed to be more obvious so everyone would catch that.
It did feel to me like things may have been cut to keep the running time more reasonable, and I'm guessing that may have been one of them. I wouldn't be surprised if somewhere there exists a 3-hour version of the movie.