After breaking her leg, 'Smith' repairs her leg and drills a plate over the wound to protect it. The next time you see the injured leg, Atlas once again has an open wound.
Shortly after the crash landing -Jennifer's nails change from being smooth and polished to being natural.
After landing, Atlas locks in her boots so she can operate & walk 'Smith'. After injuring her leg making walking impossible 'Smith' walks, runs etc without needing Atlas to control it. Later on in the movie she is seen 'running' in 'Smith' even though when out of the suit she can barely walk.
At 0:52:27 -only the lowest of sound frequencies can travel in space, far below the human threshold of hearing.
The broken bone is analyzed as a proximal tibia fracture, but on the 3D reconstruction a mid shaft femur fracture is visible. (The femur is the bone connecting the hip to the knee). Not very smart from AI.
From 0:11:12 -since Atlas's glasses do not distort her features they are obviously fake.
At 25:35 -just after saying "excuse ma ma'am" a robot walks through two crew members and the guy on the left is not even reacting; he continues to read his tablet.
Throughout -the humans' goal is to capture the rogue AI "alive".
Apparently robots have no electric circuits which can be destroyed by bullets.
It is not explained how the "ion bomb" detonation conveniently leaves three survivors.