Base defense. All aliens (sectoids) seem to be killed, but that doesn't end.

[Jstank]

I refer you to my previous idea in letting Alien food be a throwable item that has an alien attraction set to 9. 

[phi1]

there are aliens upstairs in your laboratory and your workshop, both alive and unharmed, but also unarmed, possibly due to having panicked

Thanks a lot. I was sure that I checked almost everywhere and I thought that enemies are revealed in debug mode, but there is some additional actions to be done to show them, I guess.

Have you started the campaign using the original X-Com and imported a savedgame? Or this is a 100% OXC campaign?

I'm not sure at this point. There is a possibility that I've begun with the original X-Com.

[Solarius Scorch]

I refer you to my previous idea in letting Alien food be a throwable item that has an alien attraction set to 9. 

https://allthetropes.wikia.com/wiki/Artifact_of_Attraction