Each lease has a late fee amount and a number of grace days. If the rent for a cycle is still open when the grace period ends, House Stack Pro adds the late fee once for that cycle.
Check your local rules
Many states and cities cap late fees or require a minimum grace period, and subsidized housing often has its own limits. The setup wizard suggests a grace period and keeps the fee under the cap for the few states where the statewide rule is clear (New York, Massachusetts, Connecticut, Maine, Oregon, North Carolina and Delaware). Everywhere else, House Stack Pro applies the numbers you set; it does not decide what is allowed where you are. If you are unsure, ask your attorney or local housing office.