The Man Who Was Never Born - S1-E6
Plot hole: Andro has memorized "every detail" of Cabot Jr.'s life, including his mother's name, Noel. Yet when he travels to the past, meets Noel and learns her name, he still mistakes Cabot Sr. for Cabot Jr., who isn't born yet. Having memorized all those details, he would have known the moment he met her that Noel was Jr.'s mother. Andro's confusion makes no sense. (00:28:00)
Behold, Eck! - S2-E3
Plot hole: Eck gives Dr. Stone one of his eyes so the scientist can create a lens to improve the alien's vision. At the end, Stone hands Eck the lens, but not the eye. When Eck puts on the lens, his missing eye reappears out of nowhere. (00:48:30)