When Matt's eating pancakes he pours the whole plate full with syrup... almost up to the brim. In the next scene it's just a regular pancake.
Reeves' facial hair grows longer, then shorter, several times in early scenes, despite the scenes taking place in one night and morning.
At about 6 minutes we see Will Foster through his visor / augmented reality display. We, as the movie watchers, should see everything mirrored, which is correct for the right part of the display. However, the big "BRAIN IMPRINT IN PROGRESS" is not mirrored for us, the viewers.
In the car crash scene, the car seems to go for a nose dive in the water. However, in the scene when Keanu wakes up, the car stays perfectly balanced in the water, with NO damage on the front side and only the back of the car submerged, a "perfect scene" for his kids to die drowned. Also... the car doesn't continue to dive due to water getting inside.
He has four memories and three pods. He could simply reuse one of the pods when it finishes the first run, rather than delete Zoe.
In the kitchen breakfast scene, the milk carton with sour milk reads "Milk" on the outside. However, the story takes place in Puerto Rico, so it should read "Leche."
In the car accident, there are multiple collisions with large objects; however, no airbags deployed. This is a brand new, late model vehicle. Therefore, why didn't they deploy? This is obviously a mistake.
When Keanu Reeves' character grabs the orange juice carton from his son, the juice spills out onto the table yet no one seems to notice.
At 1:19:00 (DVD Version) William is backing up the car, trying to get away from Jones. You can see wires taped to the ceiling inside the car.
When the two henchmen enter the hospital, the guard asks them "What are you doing here?" Since this is a Puerto Rican hospital, he would have asked them in Spanish ("¿Qué están haciendo aquí?)
Foster removes the memory of Zoe from his family memory maps, but what about all the dozens or even hundreds of people who may have interacted with Zoe throughout her life (teachers, friends, neighbors, parents' colleagues, etc.)? Also, in this time and age when people take countless digital photos of themselves and others, how can he eliminate all evidence of her existence from the world?
A genetic clone would not have any of the physical alterations (such as tattoos, dental fillings, scars, etc.) that the original individual had experienced during the course of a life, yet Mona's clone has pierced ears.
To add to the comment that clones wouldn't have pierced ears. It is said that the accelerants follow the DNA precisely. Not in DNA are Hairdressers, shaving razors or manicurists. the girls would have unshaven body hair.
After the accident, Ed states he could only bring three 1.7 million dollar pods (which nobody misses) as that's all there are. As Ed walks into the lab the next day he walks by several pods.
Officer Pérez and Rodriguez coming to Mr. Fosters house and asking about stolen batteries are perfectly dry, even though it rains a lot and they had to walk through the rain with the police car visible in the back. So sign of umbrellas or any other rain protection.