When Ripley goes down the power plant to retrieve Newt, Bishop leaves the platform, because "it is too unstable". He could be the one who goes back to the base and picks an alien egg. My point is motivated by:
- each synthetic man in the Alien franchise has the mission to spread the aliens, in one form or another. It's true in Alien, when Ash opens the door to let the facehugger in, and later tries to kill Ripley after she discovers the truth. It's also a fact in Alien3 when Bishop II tries to get the alien queen from the pregnant Ripley. It's also true in Prometheus and Covenant where David is clearly on the alien's side.
- Weyland-Yutani is clearly on the aim of retrieving aliens. They spend billions to achieve their goals. Why should they only trust Carter J Burke, and not have a Plan-B in Bishop?
My point is there's a hole in Bishop's calendar: what was he doing while Ripley was down in the powerplant ? It brings another question in: what were the orders given to Bishop ? He does his best to keep survivors. OK... Why ? Because if no one survives, the aim of bringing back an alien, aboard a non-empty vessel or through a salvage mission is unlikely.