Shift Into Turbo: Part I - S1-E1
Plot hole: Divatox and co. live in a submarine in Angel Grove lake. In "Hogday Afternoon", Angel Grove lake was drained to about 30ft at the deepest. The lake would have to be several hundred feet deep for a large submarine to hide there.
Honor Code - S6-E7
Plot hole: In the previous episode, when Jimmy offers to apologise to everyone about stealing money to pay back gambling debts, Eugene tells him not to, since if the other firm members found out they'd be obligated to report the theft, which could endanger the firm. This episode, Eugene justifies reporting Jimmy to the bar for saving the boy's life against the client's orders by shouting about Jimmy's gambling theft in front of all the firm members whom he previously said he didn't want to know about it.