At the beginning of the episode right after the scene where the research vessel sees the mysterious alien ship, the scene changes to Samantha's kitchen where she's boiling water for a pasta dinner. A pasta jar can be seen right next to the boiling pot of water, open and ready to use. The next camera shot is of Sam standing at that stove-top counter, but she then responds to her daughter, Ruby, and turns around to walk to the island counter where suddenly the pasta jar now is, unopened. Sam's dialogue continues where she says dinner won't take long to cook, and she then takes the jar of pasta, opens it and walks it over to the stove-top where she sets it down in the first cut-scene's original location.
As Sam is driving into the desert (around 24 minutes), the road seen from her point of view is in good shape with white fog lines at the road's edges. The road as seen from the air is somewhat dilapidated and has no white fog lines.
J'onn phases with Supergirl and Wynn in this episode. Phasing is an ability that J'onn (and other Martians) possess in the comics. However, they are not able to bring others with them. Phasing is part of their physical abilities, tied to their shape-shifting abilities, and not something they are able to give to others.
When Sam is driving into the desert, the camera shot has her driving southbound and then double backing in the exact same location. Either the character direction was to wander around aimlessly or they were only able to shoot from that exact location and angle.