I still don't get why Jack's semen was found on the scene

Well, I didn't watch the ending because I got annoyed with the movie, so I apologize if this was stated in the movie. But in the book, the semen was not clearly identified as a match to Jack, and was said to likely be a match to someone related to Jillian. So it was just hey, here's a bunch of evidence against you, plus something else that MAY have been something else to prove your guilt. Though throughout the book, it was indicated subtly that there had been long term sexual abuse, so it could have happened earlier.

How could the dad have been in the woods with the girls that night? While they were doing their Wicca ritual, the dad was leading a meeting and trying to drive Jack out of town.

~Vivian

I haven't seen the ending of the movie yet because it's on, but like judithsr said throughout the entire book it's implied Amos was raping his daughter Gillian. I don't know if it's shown in the movie, but in the book Gillian has a sudden rage of hate and urge to kill her dad. She "wondered what it would be like shoot [her dad] in the head." We find out later it's because he's been abusing her.

The semen on Gillian's thigh is her dad's from him previously raping her. He obviously had a history of rape since Addie revealed to Jack in the book that she was gang-raped at sixteen by Charlie, Amos, and a third guy and ended up getting pregnant with Chloe. I don't understand why the movie didn't have Addie say she was ganged raped by the three instead of just one person... though maybe once I get to the ending I will understand :)

Anyway for the main post of this question... in the book a DNA analyst does a test on the semen and mentions to another character there aren't four district numbers at some location on the DNA. She is surprised because with two unrelated people there should be. She suggests maybe Jack is a relative of Gillian's or a relative of Gillian's raped her. Apparently Jordon didn't catch on...

As for the other point mentioned, I found this on a forum "The book states that in the six locations tested in the semen sample, Jack was 740,000 times more likely than someone randomly selected from the population to have contributed to the sample. Well, Amos isn't representative of someone that would be randomly drawn from the population. He's a relative of Gillian's, so that statistic no longer applies."

I've read all the comments in this thread and I still don't get it about the semen. The lawyer guy asked: "Why was your semen found...?" He specifically said "your". So how could that be possible?