When Michael Clayton spots Arthur Edens in the back alley, we see Arthur carrying a bag of bread. In the beginning of the conversation, one bread in the middle is missing its top, which apparently may have been eaten. In the following shots, we see the same bread full, without the missing top.
When Michael and Marty are having the conversation in Marty's home, the glass doors on the bookcase behind Marty change positions numerous times during the scene; probably to avoid reflecting the camera and crew in the glass with each new camera position.
When Clayton is in Arthur's loft and he picks up the red book from the coffee table, you can clearly see the folded slip of paper sticking out from the bottom. A moment later, as he's flipping through the book, he almost doesn't see the paper because it's all the way inside.
When Michael Clayton asks Marty for a loan, a crew member can be seen in the reflection of a wooden door over Michael's left shoulder. The crew member moves back and forth during the scene, making it clear it's not one of the actors, who are standing completely still.
The cop tells Michael Clayton about Arthur's death, "There were pills all over the place." This would not have been possible, whether they were scattered on the floor or, as the murder scene suggested, shaken into the sink, because the bathroom was flooded, presumably from the sink where the pills would have been taken. The water would have dissolved any pills in the time it would have taken to flood the downstairs.
It is stated that Michael started with the firm in 1990, and has been with them for 17 years, making the year 2007 as expected. His birthday is also described as being in 1959, but at another point while speaking to Marty he reflects on his state in life and claims to be 45 years old - he should be 47 or 48. He may, however, be exaggerating his youth.
After the bomb explodes and Clayton's car is burning, he throws his wallet, watch and personal effects into the burning car, apparently to make it evident that he was killed in the fire. But any investigator would quickly notice that no charred human remains were present and the story wouldn't hold.
In the early part of the film, during a drive in Manhattan, a tree can clearly be seen in vivid bloom, which occurs in Spring. However, the rest of the scenes take place in a Christmas Season time frame, evidenced by the numerous shots with lit trees, and decorations. As well, the grass is dead in most rural New York scenes, and actors' breath is clearly visible, once again suggesting late Autumn, or early winter.
Following the final encounter between Karen and Michael, Karen can be seen looking off into Michael's direction as he walks away from her. However, in the next shot, she's looking straight ahead, 90 degrees to the right of her initial stance.
During the conversation between Karen Crowder and Mr. Verne, in which she authorizes Verne to take action against Clayton, her left coat collar switches back and forth from being turned up to laying down between her over-the-shoulder and frontal shots.