It's a minor thing but, the squashing of the cricket. Johnny didn't mean to do it...
Johnny Five: Error. Grasshopper disassembled...
Johnny Five's apparent demise in the first film. Yes, it's a Disney Death, but still... Even Howard seemed pretty despondent, (and not just for losing tech worth millions of taxpayer dollars) just before firing Skroeder.
Howard: Years of research are down the tubes, and you're happy as a pig in slops. Skroeder: (still smugly proud, and oblivious) Just doing my job, sir. Howard: Maybe from now on you can do it somewhere else.
Short Circuit 2:
During another reading binge at a bookstore, Johnny finds two books that he says he will read "very carefully". After he is arrested by the police, and treated as property rather than a person, he's shown reading one of the books slowly and carefully, rather than flipping through in seconds like he normally does. The two books? Frankenstein and Pinocchio, both about man-made creations who were brought to life, just like Johnny himself.
Johnny's understandably hurt reaction to learning Fred was going to sell him out (literally).
Johnny: Fred wants to sell ME?'! Fred: (laughs sheepishly) Oh, J-5, c'mon, it's just a figure of speech. Johnny: Am not property, Frederick! One whose person is under control of another as master, is a SLAVE!
The look on Fred's face when he finally finds Johnny ... and sees the condition he's in. His expression goes from joy to horror in seconds.
Johnny getting Fred's name wrong may seem funny, until your remember some of his brain is still damaged.
Fred: Are you okay? Johnny Five: Functioning 100%. Perfectly ko Derf. Fred: It's Fred. Johnny Five: That's what I said, Derf.
The aftermath of Johnny Five's beating by the bank robbers. Also, near the end, when Benjamin tries to revive Johnny Five's battery power with a defibrillator, just after catching Oscar.