An alien morphed into one
The Alien that came from Foster? Cameron states that an Alien needs to be nursed by other Aliens to become a Queen. This statement goes hand in hand with Aliens, given that it wasn't just Newt's dad that got infected and there were already multiple aliens beforehand to establish a nest and nurse a young alien into a Queen. A lone Alien suddenly morphing into a Queen, however, is an unstable claim to make and it has never been demonstrated in the movies or even given as part of the series canon.
...or if you want to go the royal facehugger route..
All we know from the films is that the Queen can presumably carry an insurance egg that can both lay a normal alien and a queen. The problem is is that Foster's facehugger isn't mentioned escaping or mutating in any of the audiologs. It also looks like a normal Facehugger, not the Royal Facehugger we've seen in the behind the scenes stills of Alien 3.
..first alien made one of those
Which would mean an unexplained landmark life cycle mechanic that allows a lone drone to make a royal facehugger. Again, not part of the series canon.
Just because the source of the eggs isn't shown doesn't mean there's a problem, there's no source for the eggs in Alien within the context of just that movie either.
Yes actually, the first film has Eggmorphing to explain its eggs.
The fact that the Queen was or wasn't shown isn't the main problem, it's her not fitting in to the overall context of the story period.