Only the Bad Come to Sonora - S4-E3
Plot hole: Manolito trades clothes with the poor peon he meets on the road. But at the end of the episode, he has the same clothes that he gave away earlier (his usual outfit) back on again.
Plot hole: When Nadia had been held captive in The Village, how did she get word to her accomplice to be ready at the exact time, in the exact location, and with a packing crate ready, and a whole series of transports arranged? Even if Nadia was in on the ruse of conning Number 6, wouldn't he be suspicious?
The Spores - S2-E7
Plot hole: Hal and Roy could not open the spore case with an electric power drill, but later a married couple pops it open with a hammer and chisel, then much later some children acquire the case and easily open it.