While I don't know what the rule was in all ports, at least in Charleston Beginning in Charleston, and expanding to many other Southern ports over the next few decades, the law required that free black seamen whose ships came into port spend the night in the city jail. This law was in place from about 1822 onwards, part of a number of laws put in place following the quashing of an alleged slave uprising that was being orchestrated by a free black man named Denmark Vesey (coincidentally one of the founders of the Emanuel Church that was the location of the recent shooting). The laws restricted further what rights were held by both free and enslaved blacks in the city.

Edit: Doing a bit more research on the law itself, see below for some expansion on the matter.