I just watched Revenge of the Fallen & Simmons does in fact say to Sam "You're the case that shut down Sector 7.", so having a Sector 7 logo on the sign does in fact conflict with the fact that wer're supposed to be in NEST, NOT Sector 7, so it's definetelly a mistake.
Could it be possible that when designing the ride, they were considering Sector 7 to be the setting for the ride, but later switched it to NEST?