Why does the ruin recognize Orta and Lagi as a "unauthorized molecular structure"?

I think this is because of Orta. She doesn't seem to be recognized by the security system (Lagi is recognized as the master), although this was the place were she was created according to Abadd. This is strange especially given the fact that the system uses Azel's voice. I'm afraid I can't answer this question.

Abadd says Drones were never meant to reproduce? Why? And who's the exception?

Drones were the slaves of the Ancients. By not allowing them to reproduce, they were certain they could could keep control over them. As Abadd said, they live as slaves and die as slaves. However, Orta is an exception to this rule.