In quick battle there were no civilians present when I tried this. (I didn't use his save file.) In debug mode after the computer is done moving the aliens and before I press end turn the last alien is still selected (indicated by yellow arrow). The center on selected unit will center on the alien with the yellow arrow. The select next unit will just deselect the current unit. Maybe it would have selected a civilian if one was present, I don't know. I can still manually select aliens with the mouse though, which I wouldn't think would work if it was the civilians turn. In playing around with this, when I pressed end turn with an alien selected I think it then went to the civilian turn as I wasn't able to select any alien or x-com unit. As there were no civilians I wan't able to confirm that it was the civilian turn. Pressing end turn a second time, advanced the turn number (shown on the press button to continue window) and automatically selected an x-com unit as expected. It seems to me that in debug mode the alien turn doesn't end automatically without pressing the end turn button before going to the civilian turn.
I was surprised yhe1 had trouble finding the last alien in debug mode. Not having the FMP, I didn't try his save and just used what I had (OXCE 6.3.4 with X-Piratez mod K2) and quick battle in debug mode. I would have expected him to see the last alien indicated by the yellow selection arrow and centered on the screen during the alien turn. Even if it was the civilian turn, he should still have been able to see the alien's location on the minimap.