Pred: 'Inhabited' can mean a world full of wildlife. But even if we presupposed an advanced civilisation, it could be...
* Subterranean civilisation. Some species just prefer living beneath the ground. If the egg chamber was artificial, this might even prove that.
* Buildings on the surface, but covered by fossilised hive resin - the bone-like rocks are effectively covering what once laid beneath.
* Buildings so old, that they literally collapsed into rubble or corroded away. It's useful to keep in mind that it's only things made out of stone which are likely to last down the ages.
* A limited colony - just like Hadley's Hope was. Everywhere else being a once-thriving ecosystem. As the centuries wore on, nothing would be left.
As I say, I'd prefer if it was always uninhabited, but I also love O'Bannon's idea for what it might have once been. Especially how he wanted the planetoid to literally tie into the Lovecraftian mythos amd have the Alien a "blood-relative" of the nightmarish star gods. If a future story ever wants to show LV-426 as having once been a lot more active than we've ever seen it, the above methods could be how it's done.