Biggest Plot Hole
There's a few threads here about various plot holes in the film, (such as Sorority Kayleigh not remembering any abuse and Prostitute Kayleigh does remember it), but to me the plot hole that ruins the movie is that in the Sorority Kayleigh timeline Evan gets sent to a maximum security "slam your ass" federal penitentiary for the murder of Tommy.
There is simply NO WAY he could have been convicted of murder in what was so obviously a self-defense situation. Tommy had just been released from a psych ward, his fingerprints would have been all over the bat, Evan would have had huge bruises from where Tommy had hit him with the bat (assuming he didn't have broken bones), it would have been easily proven that Tommy was the one who smashed up Evan's car that same evening with the same bat, Kayleigh was a witness to the attack, and there were probably other witnesses off camera as well. On top of that Tommy was a known pscycho who had spent time in juvenile detention and mental institutions whereas Evan was a popular college student.
I'm willing to accept the premise of time-travel through journal entries, but the idea that any jury could convict Evan for murdering Tommy stretches my suspension of disbelief beyond the breaking point.
P.S. Before anyone says "He was there awaiting trial", they don't send you to that kind of prison when you're awaiting trial. What his mother was talking about when she visited him was an appeal of his conviction. When you're awaiting trial you're sent to jail, and Evan would surely have been released on bail before his trial. But lets face it, even the idea of him being charged with murder is far-fetched.