For a break to appear when clocking in and out, you must clock out when the break starts, then clock back in after the break ends. The next time you clock back out, this will register as the end of the shift.
If the employee realises they didn't clock out for their break on the same day, they can clock in and clock out at the end of the shift. The admin (or the employee if they have been given access) can then edit the clocked times to show correctly when the break was taken.
If the employee doesn't realise they didn't clock the break until the next day (or later), they can't add one in, but you can adjust the end of shift time to account for the unpaid break - the end time of the shift wouldn't be accurate, but the total number of worked hours would be correct.