As Max and Logan are leaving the city, it shows a close up of Logan in his car, the front of the car we can see is yellow (this may be presumed to be because of the fact that he had to abandon his car in 'Exposure' at the prep school where he found Ames White's son). A few shots later, it shows a wide shot of Logan coming upon Max's motorcycle, and he is driving the blue Aztek that he usually has.
The NFPA (National Fire Protection Association) standard warning symbol as Joshua enters Terminal City through the fence includes the numbers 7 and 9. NFPA ratings range from 0 to 4. In addition, the corrosive warning COR is in the yellow (Reactivity) square, rather than the white (special warnings) square, where it belongs.
Sam's existence as a X5 who didn't escape in 2009 means that Lydecker should have recognized Max in the Season 1 episode "Prodigy". Even if he hadn't met Sam in person, it would be unforgivably stupid of Manticore not to give pictures of her to the man tasked with hunting down her twin. (This plot hole wasn't already raised by the existence of Alec, since "Pollo Loco" never established whether Lydecker knew what Ben looked like.)