Minor Plot hole: There is a problem with the safe room in the 3rd level. If the projections and the Inception team were, at first, supposed to travel through a maze to get there, why was the room leading up to the safe room windowed ? What would stop the projections or anyone to simply break the glass and get in ? After all, Cobb destroyed the glass to kill his wife's projection and got in at the same time as the other team members using the short-cut.
Minor Plot hole: One of the rules of Inception's universe is that what happens to the dreamer's body will affect the physical aspects of his/her dream. Thus, when the van is falling in the first dream level, the second dream level has zero-gravity....but then, for no reason, there is still gravity in the 3rd level while the dreamer of this particular dream (Eames) is experiencing zero gravity. Even if the effects had to be smaller than in the second level, a change in gravity had to happen in the 3rd level.
Major Plot hole: Arthur should have awaken from the second dream when the van was starting to free-fall. It is shown that in order to wake up from a dream (with the compound ) your body in the dream above must be experiencing free-fall while you are asleep. No one wakes up because they are into a deeper layer of the dream and thus need synchronized kicks in order to wake up. Arthur does not need that however. He is not in the third level. Based on those rules, it is impossible for Arthur to stay asleep in the second layer.
Plot contrivance: Instead of ONLY asking a yes/no question about the shortcut added to the 3rd dream level so that Saito and Fischer could reach the safe quicker, Cobb asks Ariadne to tell him what it is (without explicit details).....so that she can then tell the others. There was no reason for Cobb to ask anything on what was added; even if he only knew that it was an air duct. He simply had to know that a shortcut existed and let Ariadne contact the others without being the dangerous middle-man. He shouldn't even know it was an air duct.
Plot contrivance: In the first dream sequence, Cobb does not want to wake up in order to read Saito's confidential documents. This thus obliges Nash to push his chair into a bathtub full of water to wake him up. However, his sensation of free-fall should have been enough to wake him up before he hit the water (as it is seen with almost ALL other characters in ALL the other dreams). The sequence where the Japanese-styled building explodes with water would only have been possible if Nash poured a water bucket on Cobb's head or something similar.