When Walt sits in the bar at the end, he orders a neat Dimple Pinch. The bartender pours about a fifth of a glass. Two minutes later there is a shot of the glass, which is now not only smaller than the last one, but also half full. The scene ends with a shot of the glass Walt ordered from the beginning combined with cops in the background. This continuity error was caused by the loss of a canister of film and parts of the scene having to be re-shot.
When Saul gets his photo taken in the vacuum shop, the image that is applied to his driver's license is not the one taken just seconds earlier.
When Ed is going to pinch Walter's arm to give him his chemotherapy treatment, there is no rubber band to make his arm's veins bulge. In the next shot, it appears.
When Walter goes to check out the TV in the hideout, there is a box with the DVDs placed next to the TV. In the very next shot, the box is on top of the TV.
When Walt leaves his hideout and exits the gate to head towards the nearby town, tire marks from his recent visitor's car are visible on the snow, but the marks disappear in the next shot.
Law enforcement identified as "Sheriff" arrive at the New Hampshire bar to apprehend Walt. In New Hampshire the county sheriffs perform duties related to the court and criminal justice systems. Local and/or NH State Police would have dispatched in such a situation.
The SUV the DEA agents were using to drive Marie home had a New Mexico license plate. As it is a DEA vehicle, it should have US Government license plates.
During the end credits under the Co-Starring list, Todd Terry's character is listed as "ASAC Ramey." However, the character he actually plays is that of Special Agent in Charge (SAC) Ramey.
When Skyler is back home after being interviewed by the authorities, there are three men in Holly's room. The scene before shows law enforcement watching the house seconds before where they report "no activity". Any law enforcement would be watching the house for a 'known criminal' to return from multiple vantage points. It would be ludicrous that three men dressed in black could enter a surveilled home to do what they were able to do under the circumstances.
One of the deputy sheriffs who enters the bar identifies himself as "police"; police departments and sheriff's offices are two different things.