At first I assumed I simply missed the death of my dupes (as the sound notification is easily missed IMO) but after looking at my newest base's Colony Summary I am 110% certain that there's some bug in the Duplicant count for the Colony Summary.
In the pictures below are two bases where the dupe count spike and then falls back, in the span of 2 Cycles. Even if I was to miss a dead dupe, it still doesn't explain how I, in the second picture, went from three (3) duplicants up to seven (7) in one Cycle, and then managed to murder 3 of them in a genocide before the next Cycle...
Something is clearly wrong here.
Start a base, play for X amount of cycles, check colony summary, probability of some "ghost duplicants" increase over time. I think saving the game, maybe loading it up once or twice after (as I wanted a more efficient start) makes the game add up new duplicants from the "different" colonies.