Previous scripts told of Alien Soldiers/Drones/Whatever-You-May-Call-Them, that hid among the Sulaco along with the Queen. Would it be that difficult to extrapolate that idea, maybe without explanation, grabbed two eggs, and planted them and sealed them near the freezers. In the resulting explosion they (or one, died) died, releasing more acid they ate through the Sulaco, exacerbating the fire. This actually might have made the descent worse, if the escape pods weren't already rigged to be unsafe by Weyland-Yutani.
It could be a number of things. But the fact they had at least one or two of the bastards on the ship hiding throughout the scripts, gives credence in my mind that it wasn't only the Queen that snuck up in the Sulaco. As for a total scan, you know how Aliens are. They're a little Mary-Sue. "They don't show up on infrared at all." They could have waited for them to go into hypersleep, noticing they're not moving; and planted the eggs to make the LV-426 hive survive and continued to flourish.
That's always been my take on reading the scripts. They did the best they could to root them out, but xenomorphs are sneaky strategic bastards, and I wouldn't put it past the Queen to bring one or two m8s with her to seal the deal. Distract them with a fight, while the the other one or two hide for the right moment.
This is all my head canon, but the fact that even Ward brought this up suggests that, well. The only answer left is off screen, a xenomorph planted the egg, and died in the resulting electrical fire.
