I haven't looked at your save, but there is an event called "Abandoned Device" in the Starting Events which gives a class 8 planet with 5 population. The planet can only support 3 population, so the excess will die off at 0.1 per turn. Perhaps that planet came from the event, and you found it before the die-off was complete.
Also, the AI may have decided to move an excess colony ship with 1 population there. It would raise the population from the normal 3 to 4. You would have to get there right after that happened or the population would have decreased to 3.9 and would show as 3 unless you looked at the details of the planet. I don't think you can see those details unless you had good espionage against them.