The Rule 5 draft is held every year in mid-December. Teams are allowed to select players from other organizations that are (a) eligible to be taken and (b) not on the other organization’s 40-man roster. The 40-man rosters for this exercise must be set in advance (in 2019, the deadline is November 20) and can generally not be changed after that date.
For most organizations, the 40-man roster is sufficient to protect all of the players on their major league roster and all of their “top” prospects. But occasionally a team has such a deep minor league system that setting the November 40-man is problematic: they are forced to leave valuable players off the 40-man, and risk losing them for only marginal cash considerations.