This is kind of the issue with trying to tell the same story multiple times through multiple mediums. In neither WC3 nor the novelization is anything mentioned about seeing cursed grain crates outside the city. Even in the instance, there's no mention of them since the exchange at the gates is copied verbatim from WC3. The games have to make it into a playable mission so they take A LOT of liberties with the story.
In WC3 Mal'Ganis makes his way throughout the city with an entourage of ghouls and aboms, and he can be encountered and killed multiple times throughout the mission. You also see people who are clearly just walking around sick well before they turn. In the scenario, Arthas also has part of his forces building camp nearby, which of course doesn't match later iterations of the event. We also know (after the fact) that Mal'Ganis isn't trying to raise an army for himself or kill Arthas, but rather just goad him to go to Northrend.
In the Caverns of Time instance, the city has cult of the damned necromancers, nerubians, and other types of undead doted throughout. Arthas also leaves most of his men outside the gates and only enters with the player group. And unlike WC3 where you're trying to kill villagers before they turn, in this scenario Arthas only kills 2 humans at the gates and then the entire city simply becomes ghouls and zombies which means there is NO CULLING! Yeah, I wouldn't take anything in the Culling of Stratholme instance at face value.
In both game versions, Arthas also leaves most of his forces posted outside the city. In the book, most of the troops leave with Uther and he proceeds with the purge with all the ones who remained.
The best source is still the book. Its whole point is to depict the story without worrying about quests, balance, and other game mechanics, as well as give us the inner thoughts of the main characters along the way. The book makes a point of noting that the smell of bread (which Arthas keeps smelling even hours later when the blood, smoke, and time should have drowned it out) is what convinces him the city is infected. No grain crates, no zombification. It very clearly states that Arthas killed mostly living humans, meeting only sporadic zombie forces. He only finds out Mal'Ganis is indeed there a while into the slaughter, and only confronts him at the very end (he never witnesses Mal'Ganis gathering undead, and indeed finds him alone before he teleports out).
The book most strongly supports the story that Arthas made a rash decision with very little evidence, killed mostly living humans who he could not have known were infected or not, and the ultimate plan was for Mal'Ganis to trick Arthas into following him to Northrend, not raise an undead army and spread across the kingdom.