As seen in the mind meld sequence, Voyager 6 evidently had a Pioneer Plaque, so it's perplexing how V'ger came to the conclusion that the carbon units that were depicted on or in V'ger itself were an infestation. Seeing them as pets of the Creator, for example, would have been more reasonable, given that V'ger was still somehow unable to understand this thing, life, that it had digitized zillions of times before.
And that's not even getting into the fact that V'ger couldn't possibly have learned all there is to know about this universe if it couldn't understand regular life, something it had digitized many times before. Having knowledge that reaches the limit of this universe implies understanding life in this universe. Spock's supposed to be a supergenius, one who's realized his humanity by that point, so saying that Spock's wrong in-universe is a cop-out. The fault is the writing. What V'ger is supposed to be just doesn't make sense.