While Holly is trying to fix the issue, she is sitting at Lupo's desk at GD. The name plate on the desk says DEPUTY J LUPO. In the altered time line, Lupo is Security Chief at GD and her desk nameplate would reflect that.
When Kevin shows Jack the songs playlist the "Song Name" and "Artist" titles are above the wrong columns, ie., the left column contains the Artist's name, yet it is headed by "Song Name".
When Alison pulls over at the end, she's attacked from behind and injected. However, there's no place for her attacker to hide. There's no vehicles except those in front of her when she stops, the left side of the road is a vertical cliff, the right side is a significant drop. The only place anyone could hide would be down the hill, but he wouldn't be able to get up and behind Allison that quick without going at a sprint and being completely visible.
It seems odd that no one noticed Zane burning down Jo's house, and that no one called the fire department.