Well they still don't know precisely what went on down there. The entire team that was sent down there to find out are dead. I don't think they knew exactly why it was suddenly locked down in the first place and they sent the team down to find out.
Matt is being put in the Nemesis program, which suggests that they still want to continue the research and development of viral weaponry. So to continue that research, they need to find out exactly what happened in the Hive and why so they can establish what not to do next time.
Film vs the Game
Why does Nemesis still have orders to eliminate S.T.A.R.S. members in the film? If the events of Resident Evil never happened in the movies (and it's never even hinted that they did), then none of them has any knowledge to suppress about Umbrella's chicanery.
That one at least has a point to it; it's a test. I don't remember the line but Mr. Evil Scientist said that the S.T.A.R.S. are the best of the best and they want to see if Nemesis can take them.
Except that Nemesis had just been equipped with a minigun so powerful that anyone could have taken the S.T.A.R.S. guys down with it. Really, the "test" was far more a test of the minigun than the giant dude lugging it around.
And it actually is hinted that the first game happened. Jill knows about the zombies. Despite the fact that ANYONE in the real world would see "they didn't go down after two shots to the chest; SHOOT THEM IN THE HEAD" in the universe of the films, this is something one only realizes after having dealt with them firsthand.
It's possible that Isaacs knows that Alice and the clones have genetic memory, and if an Alice clone shows full awareness of events enough to actually overcome the test fully, she would be a "complete" clone, possibly viable as the one with "cure" DNA Isaacs is looking for.
Shouldn't the boat at be overcapacity?
How did they fit over 2,000 survivors in that ship?
Being that the "survivors" were kept in stasis tubes rather than conscious, it was likely we only saw one "floor" of the survivors kept in tubes.
The Injectors
Why did they give a whole bunch of people P-30 injectors? It's too inefficient in [RE5] to be used on more than just Jill.
And also, why are all of the injectors really visible? The most glaring one in particular is Jill's, since she's apparently going into combat with it in plain sight on the exposed part of her chest.
