
Jane dies from suicide by hanging herself after realizing that she's pregnant with Luke's baby. Keep in mind, Kenny was a well known character since Season 1 and the way they killed him off is nothing but disappointing and a bad way for a beloved character to go out. Kenny is sent flying out of the windshield, paralyzed from the waist down and ends up getting eaten by walkers. Kenny dies from a car crash after Clementine looses control of the car. While Kenny and Jane do come back in Clem's flashbacks, they're immediately killed off and their deaths feel forced and are pretty lame. Proving that some choices don't even matter. But if you take Conrad's deal, Gabe will complain to you about being a coward. When you kill Conrad, Gabe will complain to you about why you killed him. How did Clementine not get infected after kissing Gabe, who got bitten? While that is not how the bite infects you, Clementine could have gotten sick since Gabe is technically sick from the walker bite (if you choose to go with Kate). It's strange since Kate was off-screen during that time, so this could confuse the player. When Javi and Clem look for Kate, somehow Kate turned into a walker.
If you don't vote and let the timer run out, Javi gets shot in the head.
When you try to "save" Avi or Tripp, choosing to save one of them, actually results in the player's choice being shot in the head. During one of Clem's flashbacks with Jane (if you go with Jane back in Season 2), somehow Carver's face still has his mouth and stash intact. Back in Season 2, Kenny smashed Carver's face in with the crowbar to the point of his face just being flesh. A number of plotholes due to poor writing.