When Maggie visits Alex in her apartment. Alex puts the pizza on the bench, opens the box to look at the pizza, then closes it again. When she closes it the flaps of the pizza box lid are inside the bottom but in the next shot the box is sitting just open with the lid flaps sticking outside the box.
The premise is that a bio-weapon to kill all non-kryptonian aliens was developed by Krypton's scientists, and released on earth. The logical problem with this is that Humans are alien to Krypton, as such the weapon should affect them but it does not.
Any virus developed on Krypton to kill all alien (i.e. non-Kryptonian) life forms would kill humans too. After all, anyone from Earth would certainly be aliens on Krypton, hence susceptible to the virus.
At the beginning of the episode, James and Winn argue about who gets to tell Kara that James is the Guardian; why they're bothering to whisper is a mystery, since they both know she has superhuman hearing. Even more odd is the fact that she doesn't seem to hear them, even though a similar whispered conversation in "Blood Bonds (2016)" is how she discovered J'onn's real identity.