The scene where Doon is watching the boat follow its track, the boat automatically launches into the water. Yet when the three get into the boat, the boat does not launch until Doon pulls a lever.
Lina delivers her message to Seely Schnapp. During their conversation the wooden paddle in Seely's hands suddenly is turned upside down.
Clary claims to have heard about Lina's messenger job from her former classmate, who now works at the greenhouse. However, Lina was originally assigned to work in the Pipeworks and ran straight home after swapping with Doon, meaning her classmate couldn't have known that she became a messenger instead.
When riding the boat through the flume, they come upon an obvious drop. Water is pouring over the edge. But, when they land in the lake after the drop, there is no water pouring, over them or behind them.
(at around 20 mins) As Doon is walking to look at the Generator room, a girl in full orange work gear and yellow boots walks across the control room and towards a hall. The shot changes to the door. Then when it goes back to Doon, the same girl (orange gear, yellow boots) gets up from the left and starts walking across the room again, before the shot changes back to the door.
Canned food - especially pineapple - cannot survive more than a few decades.
Lina requires both hands to climb a ladder with a 4-5 year kid (Poppy) hanging from her neck. A kid of that age does not have the arm strength to carry it's own body weight.
(at around 34 mins) When the girl shows the piece of glass from the box to her friend, she says "it's so shiny", this does not suggest she has never seen glass before. When glass ages in the open it slowly turns an orange or brown color, like those in the city. However, this piece by virtue of being inside the strong box has stayed clear, and it isn't glass.
(at around 29 mins) When Looper gives Lina a message for the mayor, he says: "Your ship is in." In Ember they don't know what a boat or a ship is, because all the knowledge of the world above has been lost. So you might think it odd that they might know the meaning of a phrase like 'your ship is in'. But the English of today contains many phrases which are perfectly well understood despite people not knowing their origins or even the meanings of words in the phrase (eg "hoist by your own petard"), so it's actually quite normal.