"They Did What?" was originally written and produced as the ninth episode of season 5, but held back when the episode order was expanded from 10 to 12. The actual ninth episode, "The Trial of Jim Gordon", is written by Ben McKenzie and directed by Erin Richards.
The title of this episode references the line that was said by Nyssa when Angel Vallelunga called to tell her about the greenzone destruction that was supposed to happen got halted by Bruce and Selina.
The opening of "Year Zero" took place at night, whilst this episode takes place during the day.
In "Year Zero", Penguin is seen getting ready for the battle along with his gang at City Hall, however in this episode Penguin is on his own and doesn't get ready at City Hall as it has been taken over by Nyssa al Ghul.
The Nightwing Project is a homage to the DC Comics hero Nightwing, formerly known as Robin. The device is shown to illuminate a light-blue glow similar to the main color of the DC character, as well as have the side-effect of attracting mammals such as bats.
Batman uses a similar device to attract bats in the comics, which first appeared in the landmark Batman: Year One.