Apparently this is a bug that has been reported. Here's a thread discussing it.
Based on a post in that thread, it seems that this bug was introduced into the vanilla game alongside the patch that implemented Shen's Last Gift.
However, it also seems like the bug is related to having your last soldier to be extracted also carry the VIP.
I was just doing a vip kidnap/neutralize mission, and my last soldier still in play lifted out with the VIP. I got an audio cue saying the VIP was killed (central on the radio), which I thought was weird. Then I see the VIP back at base in cuffs, and I thought well that was just a weird miscue, but then I got no intel and was told "we can't get intel from a corpse." So I reloaded my last autosave, from the last turn of the mission, and lifted off the VIP first- no problem.
If you are able, I'd recommend reloading the last save (you should still have a save from that mission), and having the soldier who is carrying the VIP get extracted not last.
Here's another thread describing the same issue. A comment recommends making sure to hear the entire "extraction" dialogue prompt before tabbing to your next soldier (not sure if you did this, but seems worth mentioning).
I think this happened to me when I interrupted the extraction of the VIP by tabbing to another unit and hitting the extract order for him too. Normally I can tab hit extract, tab hit extract , tab hit extract etc. But I think if you've got the VIP over your shoulder you need to wait till you hear the full VIP extracted prompt before tabbing to the next trooper.