When running through the hotel to defuse the bomb, Sarah Walker is running in high heels. When she jumps out of the pool, she has flat shoes. The next cut, she has high heels again.
In the car chase scene the front number plate on the Nerd Herd car gets broken, then in the next cut it is fixed, then broken and then fixed again.
In the pilot episode, a shot of the exterior of the Buy More store shows a LargeMart store right next door to the Buy More, in between the Buy More and the Underpants Etc. store. Throughout the rest of the series, the standard establishing (exterior) shot of the Buy More store showed the Buy More right next to Underpants Etc., with no LargeMart store in between.
In the first scene, Morgan is seen to be climbing out of Chuck's window. The background is completely black, however the window actually leads to the courtyard where a party is happening at that very moment.
On the way to disarm the bomb Chuck, Sarah and Casey go through the pool, since it's the fastest way. In the next scene there is no sign of water on their clothes.
Dropping a computer wouldn't severely damage a computer hard drive. At worst, it would damage the mechanical linkages inside the drive, but the physical damage wouldn't affect the data stored on the platters. The CIA/NSA would easily be able to recover data from the damaged drive.
(at around 2 mins) When Chuck and Sarah walk to the club, Casey and his team are in an SUV. When he cocks his gun, you can see that there is no clip in the handle. The reason for this is that the magazine is a post ban version able to hold no more than 10 rounds, instead of the usual 14-15. In order to use the same type of magazine they are hollowed out at the bottom appearing as non existent magazine.
During the stand off atop the building between the agents and Chuck the laser point from Casey changes from a small dot to a larger circle when it crosses Chuck's face. It's clearly a light rather than a laser.
When Chuck goes to LargeMart you can see that this is clearly a Costco, as evidenced by the many Kirkland signs in the store.
Why does Chuck never flash on Casey or Sarah? The intersect is supposed to include intelligence from all agencies, which would include the identities of those agencies agents.
On the rooftop, Chuck tells Sarah and Casey he saw the Serbian demolitions expert in the Buy More, however, he really saw him in the LargeMart.