If there were more Aliens than hosts (and I can't say such a thing ever stood out for me), then it's purely down to a production error or, if we're being hypothetical, potential 'twins'/'triplets' or whatever.
Logically, there would be no reason for them to unfreeze the Queen if Aliens were already there and the things would have probably woken up and started to attack when the humans got got too deep into the place, considering all the heat and movement which was taking place.