And Those We Left Behind - S4-E6
Plot hole: The very ending scene where Peter (in this version died in the ice as a boy so Walter's wife never met him) takes off some of the dust covers then picks up a toy airplane. The toy airplane he got as a child from ... Walter's wife when she was trying to placate him in an earlier episode for trying to run "home". This toy airplane wouldn't have been his as a child in this version of the universe. (00:42:00)
Plot hole: When Lawquane spots the droids in the field, he identifies them instantly as commando droids. But as he had left the Republic Army shortly after the first battle on Geonosis (the one which started the war) and has lived as a farmer ever since, and since the commando droids are relatively new (see "Rookies"), how can he know what they are? With his lack of battlefield experience, he should simply call them battle droids.
Plot hole: When John inserts Cameron's CPU, she restarts nearly instantly. She recognizes John right away and speaks to him by name. Yet seconds later, we see through her eyes as her system reports recognizing him, but she already does.
Triumvirate of Terror! - S3-E8
Plot hole: After Superman thwarts Lex's plan and knocks the Kryptonite into the sewers, Lex yells in frustration, splits his power suit off and flies away on a jet pack. Superman just lets him go. Wouldn't Superman chase him and catch him, especially seeing as how weak Lex would be like that? (00:07:35)