Sithandra's "feet" get impaled in multiple places by the grass. The wounds are not there in any other subsequent shot where we see her "feet."
When Sithandra is shot by the weapon fruit as a result of leaving the civilian zone, she clearly begins to fall face down, but then lands face up.
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.
When Æon takes a sample of the water in the cell, the glass is a few inches from her heel. In the next shot, it's about two feet away from her. In the next shot, it's back by her heel.
When Sithandra lands on the ground after fighting with Æon, her arm switches from being at her side to her head between shots.
DNA does not store memories. Æon could not have previous memories, nor the rest of the population having dreams of the lives of previous clones. Only Trevor and Owen are shown manually teaching their replacement clones.
There are several shots where post-production forgot to replace Sithandra's feet with hands.
As Æon is jumping across the circular openings after escaping her cell, the shoes she wears are the flat boots of the stunt outfit, and not the wedged heels she wears throughout the film.
Æon's neck freckle swaps sides in one shot, revealing a flipped shot.
During the course of the movie, there are many repeated or recycled shots.
When Æon is in bed naked, she's wearing a flesh colored G-string when she turns around to hold Trevor down.
When Trevor Goodchild is being examined by medical personnel and the medic shines a flashlight in Goodchild's eye, the size of his pupil remains unchanged, although the medic declares him medically uninjured. This type of, "non-reactive pupil," where the pupil does not get smaller in reaction to a bright light, is a classic sign of potential brain injury which any medically-trained person would know, even so, Goodchild was declared to be alright. The proper intervention would be for him to remain under observation until signs of brain injury have been ruled out. Of course, it's possible that Goodchild, being "abnormal" to begin with, has pupils which indeed are non-reactive to light.