Now most reviews of the film have been mixed or positive and so are the ones here, hicks said that there is a lot of confusion in the film regarding the hostile aliens.
Here is my little review: Good Acting, good plot, good special effects, nice characters.
the bad: causes the viewer to have more questions than answers, confusion surrounding the hostile urn aliens.
Though it is said they they may have been created for military purpose as one character mention that the planet is a R&D for bio-weapons.
Now the problem is that everyone is assuming that these creatures are supposed to be the xenomorphs and are assuming this film is a direct prequel.....they are wrong.
While it is anyone's guess about the aliens, the film is not a true prequel, yes it is in the same universe, yes it is set before Alien, yes it does feature space-jockeys But none of the events of the film leads into Alien.
1. in Alien, the space jockey is found dead and in it's chair. In Prometheus,
Spoiler
the Engineer aka space jockey is killed at the end of Prometheus in the escape pod rather than the derelict-like ship
2. In alien and aliens, the derelict is founded "crashed" on the planet LV-426. In Prometheus,
Spoiler
The derelict-like ship crashes on a planet called LV-223
3. In Alien, the cargo hold of the derelict is full of eggs. In Prometheus,
Spoiler
it is full of urns, which is actually the original concept along with squid-like creature.
4. in alien and aliens, the derelict is the only wreckage found. In prometheus,
Spoiler
another ship is destroyed with wreckage everywhere, if this the "derelict-like ship here was the same one in alien then old remains of prometheus would have been found.
Conclusion and theories.
So it is doubtful that these events are the remains found in Alien.
Theory one.
The creatures unleashed are not the xenomorphs or related to them but another bio-weapon they either found or created and were more effective than xenomorphs in terms of infection rate, however, like the xenomorphs; they got free and and killed the engineers.
Theory two.
Same as above but the creatures may be perfected versions of the xenomorph as the infection rate is faster (it can happen just through blood rather than a facehugger) and apparently the dead can be re-animated as a aggressive zombie-like being. They may be a related source to the xenos as they have similiar ways of procreation i.e
Spoiler
The squid-like creature is similar to a facehugger and impregnates the engineer.
I do have more theories but i would like to see what you lot have.