ALIEN RESURRECTION:
On the off-chance that they'll invent effective cloning technology, they keep DNA samples of Ripley on ice for a few centuries, just in case..... errrrr.......
Well, considering she and the alien fell into a giant pit of fire in Alien 3, they probably just tried to salvage whatever DNA they could find. It was all jumbled together, which is why there were so many hybrid clones in all those tubes. It probably wasn't until Alien Resurrection that they were effectively able to isolate the Xenomorph DNA.
They specified that they had Ripley's DNA stored, though can we trust anyone who gets the planet's name wrong?

Much as I love Sigourney as an actress, I really wish they had left her out of 4, and told a different story. I also hated the fact that after the work Cameron did on fleshing out the United States Colonial Marine Corps, they dumped this for the United System Military, and in one-line told us Weyland-Yutani were gone (bought out by Walmart).