It is established early on that simulated time is 10,000 times faster than real time, as the characters use the unit nanosecond like we use the second. Yet, in the one area where the characters interact with the Users (i.e, humans), the games, time passes at a much faster pace while it should be much, much slower.
In the episode "Wizards, Warriors, and a Word from our Sponsors," during the scene with the room of doors, Bob is seen without his beard while trying the first door.
In the episode "Painted Windows," when entering Lost Angles,
Glitch, who had been "melted" early in the episode, kept appearing on Bob's arm. On the Bob "stand ups," you can see when Glitch had been put there on accident.
Hack and Slash's height noticeably changes throughout the series. When they fight Gigabyte, they're shorter than Bob, when Enzo is confronted by Megabyte, they're taller than Megabyte. This isn't possible since Megabyte has always been established as being taller than Bob.
In Racing the Clock, at the end of the episode, Hack and Slash speak in each other's voices. (Hack has Slash's voice, and vice versa)
At one point in "The Tearing", when Bob destabilizes a tear in Megabyte's Tor, characters can be seen yelling at each other but no dialogue is heard at all.