Was he imagining it, or were Snape's eyes flickering towards Lupin more often than was natural?
As I understand, the sentence is saying: were Snape's eyes flickering towards Lupin more often than Snape's eyes were natural. That's why I might think 'were' should be used in the original sentence, because "Snape's eyes" is plural. But I'm not sure if my understanding is correct. How should we understand the sentence?