I'm not sure if anyone else had this happen, but apparently NPC's can also be kidnapped by aliens.
Once, I had a burglar in the middle of the night. Luckily I'd bought the alarm, so that rang and called the police. At the moment the police arrived, my sim started checking out some strange lights in the front yard. Aliens! I was a little amused by the randomness of the sims that allowed both burglary and kidnapping to happen at the same time, but ok. A few moments later, I wondered why the thief hadn't been caught yet. The officer's car was still in front of the house, so I wondered where to look for him. Then I noticed that my sim was in the kitchen, cooking something. It was a while later that I discovered the aliens had kidnapped the officer instead of my sim...
In the end, he was returned, but then immediately left, and the burglar ran. He didn't steal anything, and I'm happy about that, but it was still really weird...