In this series of three seasons, the “Jupiter” spacecraft is often referred to as the Jupiter 2. Even in the first episode, they call the ship the Jupiter 2. Is this merely an inconsistency? Perhaps, we are to believe the Jupiter was a prototype, and Jupiter 2 was the first working ship? (In general, each episode is riddled with little inconsistencies, so this would just be one more.)
If you’re referring to the recent Netflix reboot, the “Jupiter” craft are the individual family craft attached to the colony ship. They have individual numbers rather than individual names. The Robinson’s assigned Jupiter happens to be the Jupiter 2.
If you’re referring to the original series, the Jupiter aka the Jupiter 1 aka the Jupiter I was the first of the class, and was sabotaged and destroyed on launch. The Jupiter 2 aka the Jupiter II was the second produced in the class, and the first to successfully launch - for some values of "successfully*.
I always thought it was because Jupiter 1 is a planet… 
If you’re talking about that nitwit movie with Major Don Tribbiani, the Jupiter 1 was the launch vehicle (which looked very similar to the 1965-TV Jupiter 2), then when they got to a certain altitude, that all blew away and the traveling ship inside was the Jupiter 2, one of the ugliest spaceships in all SF.
And we will not speak of this again. Oh, the pain, the pain.
Then there is the name for their ground vehicle, the Jupiter 2 electric buggy, Lou.
The Chariot?!? 