I've noticed that as well, on my first watching of the movie, but given that it was not that deep a movie, I've decided that it's a plot-inconsistency and nothing more.
The virus transfers by bite, scratch,... i.e., by blood. We've seen it being airborne in the start of the pandemic, in the Hive, but only then, because it was in concentrated form. We've never seen any proof that "the land has [...] been infected".
Even if we try to justify this by the "infected soil" theory, I think we introduce even bigger inconsistencies:
How did this happen? Surely, zombies didn't bite the dirt (at least not that much), and even if it did, a bit of saliva infecting the whole city's soil is... dumb. There was no mention of Umbrella doing anything like it, there was no obvious reason for them to do so, and no such symptoms were shown ever again.
The soil is full of dead things (worms, moles, bugs, buried pets,...). If the soil was indeed infected in some weird way, we'd be seeing outpouring of dead insects and animals all the time. Just how many dogs would we have? And let's not forget cats, snakes, and other pets that must have been buried in the yards across the city.
Some of these corpses were just skeleton. How do you infect the blood of something that has no blood? How does a muscle-less skeleton move? I wouldn't accept a theory that the Umbrella Corporation was experimenting with reviving random skeletons in some cemetery.
Why did they rise exactly then, and how did they do so all at the exact same moment?
It was just to make another suspense/fight scene, nothing more. Most of the Resident Evils are fun action flicks, but I wouldn't read much into them.