We never saw the egg after the opening sequence... So who says it was actually in the escape pod or any other part of the main ship? Maybe the shot of the egg was actually a shot inside of the dropship. The facehugger(s) crawled from there to their cryo-tubes.
My ideas as to the "plothole" of the facehugger laying two embryos are:
A.) A facehugger that holds a queen is stronger and/or holds a regular warrior alien along with the queen. (We've never dealt with another queen embyro implantation, so there's nothing in the films to disprove this.)
B.) If a facehugger manages to latch onto another host before dying, it can sometimes lay another embryo. As humans can sometimes have twins, facehuggers can sometimes be created with two embryos. Or maybe facehuggers have a lot of embryos; they just die before they have time to implant them all. Another twin-like idea was mentioned as well, saying one egg could possibly be made with two huggers by chance.
C.) It was simply lost in the transition from the assembly cut to the theatrical cut. The assembly cut showed us two facehuggers, a regular one, and the newly-developed for this installment, "super facehugger". (I think that's what it's called...) So when the scene with the dead ox was cut from the film, so was the second facehugger.
I love the third film enough to not care, but I think people are a little too strict reguarding the rules of the lifecycle. These are bizarre organisms that are different from any creature we know of.
(As you can see, I'm a personal beliver in using a little imagination to close plotholes as opposed to letting them ruin a film for me...)