Despite being one of the worst of the new series (in my opinion), I don't think this was a production issue. I think the visual clue was more of a hint for the viewer and wasn't meant to be as obvious to Twilight.
The personality flips on the other hand should have been spotted. Twilight isn't the most social pony however, and may have missed it under the extreme pressure of trying to save the world. In fact, had she noticed, she may have assumed it wasn't a change but merely a response of her fellow ponies to the stress of the situation.