Maybe the Queen was not the only alien to sneak aboard the craft? Perhaps an Adult alien just happened to grab an egg or two and follow the queen on board.
The Queen has to leave her hive, and because she has the secondary set of smaller arms, she can grab two eggs to bring with her, and her bigger primary arms are then still freed up.
BUT During the scene where Ripley is being chased by the Queen, we can see her secondary hands are empty, so this does not hold. The other reason is that near the Queen it does not look like there were any more good eggs to grab any way. I think it is an optional use for the secondary arms, but because of the above this did not happen.
So where did the eggs/egg come from? Bishop? Queen? Another Adult alien that did not make its presence known?
Were there more than one facehugger, more than one egg, or a single egg with two huggers, or one egg with one hugger with two embryos?
I think it is one of the great mysteries of the Alien Saga.
It is like a Magician; if you explain your tricks it is no longer as interesting.