First, it is possible that a smaller ship have entered the system, but you simply haven't noticed it.
Second, the AI in Aurora is not actually all that good. I don't know if you have read any AARs, but entering unknown or even hostile system with gate builder is pretty much standard. In one of the campaigns, played by the creator of Aurora no less, one AI was sending wave after wave of scout ships and gate builders into enemy territory, despite the fact that they were being destroyed as soon as they crossed the jump point. Meanwhile an eighty ship strong fleet was just chilling on their homeworld.
The biggest danger posed by NPRs isn't their intelligence, but the potential that they will simply outbuild you.