But if the film is asking you to be critical of the characters?
Do films normally ask for criticism? No.
The Company, if they'd managed to get an Alien in a cage (which I seriously doubt) would have ended up with a jar on their head as well. Both the Company and Milburn are going into the unknown and failing to understand the dangers thereof, seeing themselves as masters of nature.
The Company would still survive and walk away with something, even if it isn't a living alien.
Ignoring the fact that it's a horror movie (which, obviously, Milburn doesn't know he's in) my money would be on the larger of the two organisms, the one that's sheathed in the protective armour of his space suit, with gloves the other organism's mouth probably couldn't penetrate given the nature of its orifice. The one that could easily crush the smaller organism's 'head' in its fist if it were so inclined.
So because it's a horror movie, we should throw credibility out the door? Sure, if this were a dumb-teenagers-in-trouble movie, I can accept that and even join in on the chorus of "Don't open that door!", but
Prometheus isn't that kind of movie.
Oh shit, the smaller one's freakishly strong and has acid for blood! Just like the Aliens the Company wanted to catch!
So, are you saying that this is the only small critter that can harm a human? You might want to talk to our own
Thedus about handling terrestrial snakes....