The first time I saw the passenger manifest for my ancestor's family, I was completely confused. Why would my ancestor be leaving from Le Havre France? How long did they stay there? Did they live in France? It wasn't until I started researching Luxembourg immigration that I got my answer.
Le Havre was one of two major ports of departure for Luxembourg immigrants (the other was Antwerp). Immigrants arrived by either stage coach (before mid-1859) or train (after), spent a day or two in Le Havre while their ship was loaded, and then left for the United States. The Institut grand-ducal offers a nice overview of the history.
Based on when my ancestor departed, I would guess that he - and his large family - took a crowded train through France. Their stay in Le Havre would have been as short as possible. There were too many mouths to feed. Then it was off to New York!