I found two scenes which do NOT make sense in Terminator: The Sarah Connor Chronicles.

First, Cameron did a swap on her chip with John Henry in the episode 22,season 2. Somehow I don't understand how this's possible if there's not 3rd one who makes this job done. if John H pulls out the cable on his rear head while Cameron pulls her chip out, both of them can't move. So there isn't possibility to do this unless they used the body which was restrained by Weaver (liquid metal) at the parking lot.

Second, there was a mistake on the season two, episode 11. It's about a T-888 cyborg coming back to future to terminate John Connor, but he wrongly came to a speakeasy and caused a fire that killed 43 people in December 31st, 1920. A couple decades after bla bla, he's been hiding himself in a wall for 110 years. Well, If so, his human tissue should already rots, and what we see must be a metal when Cameron digged him out, as No flesh can be fresh for 110 years in a dirty wooden wall.