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.

I've seen this also when invading planets, and always just assumed there was some sort of racial trait or tech I didn't have at work.  But I never tried to track it down and don't recall any trait or tech that would do that, so it would be nice to have an answer.

Ah, that explains it. Do they get +1 population per planet when they colonize, or is it just that they get a +1 population cap?

Oh yes I see, so the human player also gets the bonus (for a few turns or longer if he builds a city, he can also fill one or more colonizers) when he invades a planet.
It would have been more elegant to give +1 to Raw Production.
Horemvore, you know everything about the game.

Maybe it's really funny.  
Why then not just give a bonus to Raw Production more important instead of the bonus in Population that gives a weird fonctionning.
Giving a bonus to Growth Per Turn, or giving additional population in colony ships seems much more appropriate.

Movement is one of the biggest handicaps the AI gets. Its very very high on last 2 difficulties. (+1 and like 200% I think)

EDIT

Just checked and yep its +1 and +200% for both. Which is kinda fkd up...should be graded. Incredible is not that much different from Godlike. So similar infact that if you beat the AI on Incredible you will have no issues with Godlike.