When Aeon is leaping over the lethal grass and lands balanced on a corner, the overhead shot closely resembles the logo from the Æon Flux (1991) series.
In the original Æon Flux (1991) animated series, Aeon was killed at the end of each episode, only to appear alive and well at the beginning of the next. In the film, all the people in the world have died and been re-born over and over in a most subtle reference/adaptation of the original series.
Near the end of the movie when the Keeper is explaining to Aeon that he saved her DNA, it cuts to a scene where she is on a slab in the morgue. As he unzips her body bag, the "dead" Aeon flares her nostrils briefly.
When Sithandra is communicating with Monicans from the pond it is near dusk as there are long shadows and low light levels, but when it cuts to the other agent pruning the hedges it is clearly not the same time of day.
Æon Flux: [narrating]
Some called Bregna the perfect society. Some call it the height of human civilization. But others know better. The Goodchilds built Bregna to ensure us a future. They built the Relico, a memorial to remind us of what we've survived. They built walls to protect us. They tell us that outside, nature has retaken the world. But the real problems lie within. We are haunted by sorrows we cannot name. People disappear and our government denies these crimes. The Goodchild regime provides for us, as long as we stay quiet. So we trade freedom for a gilded cage. But there are rebels whoe refuse to make that trade, who fight to overthrow a government that silences us, who fight in the name of the disappeared. They call themselves the Monicans. I am one of them.