In Alien 3, Ripley has a queen baby in her. When she finds this out, she searches out the xenomorph, and he doesn't kill her. But why doesn't he cocoon her? Surely that would have been a safer option for the baby queen. Just leaving her to go free gives her the option of trying to find a way to kill the baby queen, which is exactly what she does.
She's already impregnated, so there's no need.
Newt, in Aliens, is cocooned to prepare her for any nearby hatching facehugger.
The gestation period is like 24 hours, so why bother? Most sentient species aren't inclined to self-sacrifice, and any subspecies wouldn't.
It's business as usual until mama comes home:
In the original film, the alien birthed from Kane (John Hurt), killed Parker (Yaphet Kotto) and Lambert (Veronica Cartwright), and cocooned only Brett (Harry Dean Stanton) and Dallas (Tom Skerritt) although, in the continuity of the series, their deaths are left ambiguous.
In Aliens, they killed the majority of the Marines, but they cocooned Apone (Al Matthews), Dietrich (Cynthia Dale Scott), and possibly Hudson (Bill Paxton) and Burke (Paul Reiser) (the original script and novelisation of the second film included a scene where Ripley finds Burke cocooned). A large majority of the colonists were cocooned as well.
It was about 15 people vs 100 aliens. In this film, it is one Alien versus approximately 25 people, so it needs to get rid of a lot of humans that could potentially become a threat if they work together. –IMDB