When Walter evacuates the air from the server room to kill the fire, a plastic water bottle on the table is shown to be crushed by the act. Creating a vacuum should have caused the sealed bottle to explode if anything.
Cabe states that if someone dies due to a flaw in Walter's software, quote, That's homicide, unquote. Homicide denotes intent. If charged, Walter would face wrongful death (or if the DA is strict, manslaughter) charges.
After Sly tells Walter that the game room doors are locked and the kids cannot exit, the camera focuses on the screen Walter is looking at, which is displaying the message "ANTI-TERROISM PROTOCOLS ACTIVE", misspelling "terrorism".
While Walter may not drink alcohol, he has a photographic memory and should know what a Long Island Iced Tea is.
Stella claimed to have listened to Walter's discussion on superconducting electromagnets, but then had to check his badge in order to find out his name. Even though she was obviously chatting him up in order to plant the virus, it was a slip in her methodology and also a slip that Walter should have caught.
The punchline to Walter's joke, via Bracket, should be that the cup is too big by 100%, not by 50% as Paige says.
Toward the end Walter is explaining what happened in the burning building the night before to Ray. After he finishes Ray says "DUDE it was just like that movie", implying that it was like Die Hard 1988. To which Walter replies "yeah with John McCain". Walter names the politician John McCain instead of the character John McClane.. While it is POSSIBLE that Walter has never seen the action film Die Hard, a genius with a 197 IQ would certainly know who the 2008 Republican Presidential Candidate John McCain is.