Signed a non-aggression treaty with another empire while a scout was in their space, and now it's stuck there. I imagine this is more of an oversight than an actual bug. I think when that happened in the original game, the ship was kicked back to its own space?

yes. AFAIK the "beaming" doesn't work yet correctly so the ship remains stuck until you cancel NAP-treaty..

Always figured it should just be sent to the nearest neutral sector in the direction of the home system anyway.