It's possible that there were entire sections of town devoid of human presence not just due to death and kidnapping, but also hiding and early escaped. The aliens might still not have completely overrun the entire town by the time Dallas and Co. get to the hospital. People who are hiding or far away from the characters are unlikely to have the time or inclination to make themselves known. We're also talking about a population under evacuation. There are no corridors, these victims are likely unarmed and in the open. Easy pickin's for xenos, especially if they're just killing people outright.
Then again, the predators were still alive in AVP1 during the flashback when the entire city was flooded up to the pyramid with aliens. So it couldn't have taken them long there either. To go from a handful to thousands, is the AVP way.
Plus we have to factor in a certain amount of suspending common sense for the sake of fun. It is a monster mashup movie afterall.