Wesker present in the film was a depowered clone.
Considering many OOC moments he has through the whole movie (never attempting to regenerate his crushed leg, proclaiming himself loyal to Isaacs despite calling loyalty foolish in Afterlife and so on), this is the only reasonable explanation one can take as canon. The door that seemingly killed Wesker is actually a biological weapon of sorts.
Hence why it manages to pin Wesker down so easily. There are much more than 4500 people left on Earth.
Given that the Red Queen's timer was more or less a part of Secret Test Of A Character for Alice, it would be no surprise if she deliberately underestimated the number of humans left alive and exaggerated the hopelessness of the situation to see if Alice would even bother to save the world at this point. The Bloodshot-critter wasn't just some random prototype monster.
It was actually the original Licker from the first film, which survived (albeit just barely) being burnt to a crisp on the train tracks. Having lost its tongue in the battle, it crawled back into the Hive to recover, starving and crippled by its wounds. It's been subsisting on zombies - human, Doberman, whatever it could find - down there for years. This accounts for its continued mutations, that gave it new eyes, a more human-like stance, and a fresh crop of fangs, to make up for the loss of its tongue. Alternately, the creature in the Hive was (what was left of) Spence.
Matt got attacked by the Licker and started mutating. So it's a safe bet that Spence, who provided the DNA that caused it to mutate. Survived as well. I think Alice only buried that axe in him, not decapitated him.